Niam leads them through what looks like the smaller meeting room on Atlantis -- the one where Weir had conducted her interviews of the Athosians in Suspicion (S01E05) with Sgt. Bates and where they had negotiated with Chaya in Sanctuary (S01E14), but which has not been used by them in recent times for much of anything. The room seems to have an adjoining balcony which opens up for Niam as he strides right through to the outside, and they are able to see the darkness of space outside. The city ship appears to have left Asuras and is quickly leaving their solar system, although we cannot be sure if the planet seen in the distance is Asuras or some other planet. The Ancients had settled their city on a planet with a vast ocean but it does not seem like the replicators would require water for their purposes -- or much of anything beyond metal ores. Regardless, they are all both impressed and freaked out by this unexpected sight unfolding before them.
Weir: We're in space.
McKay: The stardrive! Of course. The rumbling sound we heard. With all the ZPMs, you're able to actually fly the city.
Niam: Yes, Doctor McKay.
McKay seems once more to be quick on the uptake, having figured out what is going on and even connects it to the earlier shaking of the jail cell. He name-checks the stardrive which, as mentioned, is important not just for the resolution of this season but also to the finale of the entire show, as the plan always seems to have been to the fly the city back to Earth once their quest had led them to discovering all three ZPMs and the wraith had mounted an attack on their homeworld. McKay gives us some exposition and foreshadowing here.
What is interesting is the way they arrange themselves on the balcony. Weir is following Niam and Sheppard appears to be walking slightly behind them with McKay several steps behind him, and we note that they are not walking side by side now like they had been walking earlier. But as they make their way outside, McKay first seems to be going to Sheppard's left side but then decides to go to his right, inserting himself between Sheppard and Weir. He clearly picks up his pace to be able to stand next to Sheppard, and this may be something that they have done in Atlantis that we simply never got to see -- stand side by side on a balcony watching the night sky. Sheppard and McKay occupy the niche of the balcony for themselves, they are so close that they seem to almost bump shoulders but McKay gives Weir wide berth at the same time. Sheppard is not the only one who wants to avoid touching her accidentally.
Niam: Watch now. We're about to open a hyperspace window.
Teyla: Where are we going?
Niam: Atlantis.
Niam invites McKay and the others with him to watch them opening a hyperspace window, and even for them this is not something that they see every day. Niam seems to be speaking particularly to McKay here because it was McKay they had discovered has the ability to change their base code, which is what Niam and his faction of ascended-wannabes are looking for. They are hoping to get McKay to change their fate.
Because McKay and Sheppard are occupying the small nook in the balcony just the two of them, it makes the scene seem more than a little romantic. Where Ronon and Teyla are standing next to each other and Weir is facing Niam, Sheppard and McKay are standing together and McKay is resting his hand on the banister not to create a barrier between himself and Sheppard but to get closer to him, as close as he dares when they are around other people -- the same way he had been pressing his hand closer to Sheppard in the beginning of the episode. If McKay is doing anything, he is boxing Sheppard off from the others, and it is possible that that is something that Sheppard wants in this moment. What ever had happened in his scenario, McKay is as protective of Sheppard as Sheppard is of him.
Niam: The probes of your minds uncovered the truth, that Atlantis had not been destroyed by the wraith ten thousand years ago as we had believed. You only came to live there from your original home, a planet called Earth.
Sheppard: Why didn't you just dial the gate and send us through?
Niam: We're not taking you to Atlantis. Our intention is to destroy it.
Weir: Why?
Niam: Retribution.
Weir: For what? The disagreement you once had?
Note the way McKay puts his own body between Sheppard and Niam when he mentions the mind probes, getting protectively in front of him. Sheppard may not need his protection and there is precious little that McKay thinks he can do in this situation if the replicator did decide the attack his man, but he is still making a stand here. McKay knows the threat posed by the replicators better than any of the others, and knows that despite Niam's seemingly calm and civilized exterior that they are dealing with creatures so horrible they defy belief. Also note the way McKay is initially obscured by Weir so that it looks like she and Sheppard are standing side by side, which they are not. McKay is between them the whole time but we merely cannot see him when our view of him is obscured by Weir, which is symbolic of the subtext.
They all seem more than a little confused as to why Niam had brought them out to watch the ship take off and why they would bother flying the city to Atlantis in the first place. The Earthlings are concerned when Niam mentions that they know about their homeworld but note the way all of them respond to him confessing that their intention is to destroy Atlantis, and notice that it was Sheppard who once more uncovered the truth by asking the why question. They are all immediately prepared to defend it in their own ways, Ronon by throwing hands and Weir by trying to talk them out of it and everyone else falling somewhere between these two extremes. We see that Sheppard worries his lip and looks away, trying to figure out what he can do about it but again McKay shifts so that he is between Sheppard and the danger.
Weir: The Ancients no longer live there. We are the only inhabitants of that city.
Niam: There was no disagreement, Doctor Weir. Only betrayal. If you wish to know the truth of who we are, I will show you.
McKay: Elizabeth...
Weir: It's OK, Rodney.
Weir tries to reason with Niam, and it is interesting the way she gestures back at Sheppard and McKay specifically with her "We are the only inhabitants" line, given how the two of them had very recently started living together, no longer just inhabitants but co-inhabitants. The feelings of the replicators toward the Ancients resemble the bitter feelings that can only exist between people who have once loved each other, and Weir later describes them feeling as siblings to the humans, both the progeny of the Ancients but humans being the favoured children. But what Niam tells them also resembles the bitterness that can exist between former lovers or lovers with unresolved feelings between them, and his line about there having been no disagreement, only betrayal easily resembles what McKay had felt when Sheppard had left him to go sacrifice his life by driving a jumper right into a hive at the end of The Siege (S01E20).
It is possibly for this reason, because McKay knows exactly how the replicators must feel, that it is him warning Weir not to let the replicator into her mind again and not Sheppard. We further see Sheppard look away, almost as though he is ashamed of something, unable to meet anyone's eyes, chewing on his lip again. Some viewers undoubtedly interpret him as being uncomfortable letting another man touch her right in front of his face when Sheppard has never shown an iota of jealousy over other men giving Weir attention, ever. That is not a concern for Sheppard -- letting killer machines paw his boss might be, but that does not seem to be what is motivating Sheppard's unease here either. It is quite possible that it is McKay approaching Weir as though to put himself between her and Niam if need be that is making him uncomfortable. It is his man that he does not want the machines to be pawing. It is only as McKay lowers his hand that Sheppard is able to look up again.
Weir tells McKay that it's "OK" even though none of them know whether it is OK whatsoever to let a bunch of machines tamper with their brains using nanites, and McKay seems to be the only one of them to actually understand anything about how the replicators operate. He had watched Oberoth shove his whole entire hand into Sheppard's brain right in front of him, and that had not even been the torture part of his own experience. Weir tells him it is fine but note the way McKay then looks behind him, needing to check in with Sheppard as to what they are meant to be thinking about this. He needs Sheppard to confirm to him that they are going to let Weir do this. McKay can let her do it if Sheppard thinks that it is OK but if Sheppard had been against it, McKay would have continued arguing with her about it. McKay does not know what to think, and it does not seem like Sheppard knows what to think of it either, but it is clear that they want to have a shared opinion about it. They need to know where they stand on this together.
It is also not insignificant that they made McKay be the one to worry about Weir here. Sheppard also probably does worry, but he is in that place where he is unable to voice his concerns out of fear of stuttering. But it would have been so easy for them to make this a romantic scene, or something hinting at romance, at those "unresolved" feelings between Sheppard and Weir -- and they chose not to use this opportunity to tease there being anything between them. If anything, the scene is romantic for Sheppard and McKay who are standing in their small nook very close to each other, McKay looking back at him over his shoulder because Sheppard is standing behind him like they had been about to recreate the famous scene from Titanic here with the hyperspace colouring the sky behind them.
We see Weir grab Niam's hand right as McKay and Sheppard exchange a glance, and if we recall what we had seen in Michael (S02E18) and would see again in The Prodigal (S05E14), this is precisely how McKay had offered up his hand for Sheppard to take when McKay had finally introduced himself to Sheppard long after their actual first meeting on the Antarctic base, patiently waiting for when Sheppard had been ready to take him up on the offer. We see only their hands because this same thing had also happened between McKay and Sheppard once. McKay offering his hand to Sheppard was a moment that we did not get to witness and only know of it through its echoes but that had really started it all.
Having received the ultimatum from Kolya Sheppard heads back, wasting no time, and likely trying to feverishly think of some kind of plan, something he might be able to do to save McKay, the others, and in the best case scenario even himself from the terrible fate that seems to await them. His thinking is complicated by the fact that Lucius seems to still be trailing him, not having stayed by the gate or even attempted to leave the planet with his shield that could likely easily have withstood the weapons of the few Genii that had been guarding the gate, seeming to follow after Sheppard now like a stray puppy. Lucius is babbling, trying to make up his mind about whether to come or go, to try to help or run away, having a real moral dilemma possibly for the first time in his life.
And it is not even clear why he feels the need to help Sheppard -- perhaps he has come to care about the people of this planet even though he had seemed ready to bail just moments ago -- but more likely is that he had been looking to Sheppard for protection, and now it seemed like Sheppard was going back to the monster that had threatened to bury him alive, and so he does not know what to do. He does not want to give up his security blanket but his security blanket seems to be walking right back to the bad place.
Lucius: I'm coming with you.
Sheppard: You sure?
Lucius: No. Um... yeah, I am, I am. I'm coming with you... just...
Sheppard: Yes or no?
While it seems like Sheppard is responding to Lucius, like the two of them are having a conversation and a dialogue here, it is actually more likely that Sheppard is on autopilot, responding to Lucius reflexively without actually engaging with him. But on some level Sheppard is relieved that Lucius is there talking his ear off because it keeps some of the existential fear from driving him mad, it gives him something to focus on that is not the thought of Kolya killing McKay because of him.
Sheppard's fear of losing McKay is paralyzing, and by distracting him from it, Lucius is actually keeping Sheppard lucid -- and not unironically this is a strategy that Sheppard himself seems to frequently use with McKay. He distracts McKay from his fear to keep him functional in a crisis, under pressure, shifting his attention away from the thing that is making him afraid to the present moment, anchoring him in a way. And now Lucius is his only anchor, his only life-line in the moment, the only thing mooring him and keeping him from being utterly adrift, and Lucius is doing it both unintentionally and unwittingly.
Lucius: I... Don't pressure me like this! I'm gonna come with you...
Sheppard: Make up your mind!
Lucius: ...and I'll help you out, OK? Oh, boy -- they'd better give me a parade for this one.
Even though Sheppard is likely not thinking about it, there is a parallel here to when Sheppard had invited McKay to become a member of his team and it had been time for them to go on a mission in Suspicion (S01E05). It had not been their first mission (even allowing for 38 Minutes (S01E04) to not have happened yet, belonging to later in the season), as we had seen McKay shot with a wraith blaster when they had returned from their mission at the start of the episode. Even so, McKay had been wringing his hands nervously as they were expected to return to a planet on which they knew they would encounter wraiths, and Sheppard had parked himself very close to him, commenting that McKay seemed nervous.
McKay had been more than a little apprehensive about going back out to where they would encounter wraiths with the express purpose of trying to capture one alive, which may have been the most frightening thing he had ever been asked to do in his life. But where Sheppard does not seem to care one whit whether Lucius comes with him or not, probably even preferring that he had not followed him and telling him to make up his mind largely running his mouth with no conscious thought, Sheppard had never even entertained letting McKay back off. He had told McKay that he would come with and that was the end of the conversation, and it was never that Sheppard was keen to risk McKay's life -- even if losing McKay would only become his greatest fear later -- it was that McKay made him feel more brave just by being there. Sheppard needs McKay, he had needed McKay from the get-go, and it had never been to open doors and hack computers like he had told Ford in The Lost Boys (S02E10).
Even though the words that Lucius speaks here may all have been thoughts that McKay had at the time (or even later), he had never spoken them out loud, and he had been able to conquer his fear again and again, consistently showing up for Sheppard and the others. And the thing of it is that Sheppard was afraid too, all of it was new to him too, stepping through that gate was always taking a huge risk, and so it was Sheppard's tendency to project that had made it possible for him to manage his own fear by managing that of McKay's. By reassuring McKay he had also been able to reassure himself. And the more Sheppard had come to care about Atlantis and everyone in it, the more he had started to fear losing it all, and so he needed McKay to walk through that gate with him, to give him a reason to conquer his fear and be brave.
It is also interesting that Lucius mentions wanting a parade among these things that McKay could easily have thought when Sheppard had invited him to join his team on missions, saying the word for the second time in the episode. And it is precisely for the pride he feels for conquering himself that Lucius believes he deserves a parade.
McKay: What's going on?
Haemon: Out. Let's go!
Things are heating up in the village and the Genii brown shirts led by the soldier from Cowen's personal guard come by the cells to fetch the team, and they have no idea what is going on, getting no answers from them. McKay and the others are paraded out of the jail, and while Teyla is the first to emerge, McKay is right behind her. They are all apprehensive because it cannot be good news for them to be taken somewhere, especially as they do not believe Weir would have given in -- especially not so quickly. The men are rough with them, seemingly especially with McKay, which may suggest that he had been dragging his feet. Even though he had come out, we have noted before that McKay tends to take his time doing things and it seems he had been taking too long for the liking of these henchmen. While they would obviously see Ronon as the most dangerous of the prisoners, it is also entirely possible that these henchmen are aware of Kolya's special hatred toward this man called "Doctor McKay," and hence are acting it out on him here.
What is interesting is that as they are being led forward, McKay seems to exchange a glance first with Teyla, and then looking back at Beckett. While it is of course possible that he was merely concerned for his best friend and checking up on him, it is also possible that McKay was reading both of their thoughts off of their faces, that he needed to see their faces to know what they were thinking about all of this, to check in to see if anyone had any more idea than he did what was going on here, where they would be taken or if anyone had even the notions of a plan for what they might be able to do. But it does not seem like any of the others know any better than he does, and McKay looks lost and helpless as they are being led like pigs to the slaughter.
Lucius: I'm just spit-balling here: what if we hugged each other and the device would... would, you know, help us--
Sheppard: I don't like that idea.
Lucius: No, I know, I don't think...
Sheppard: ...and it's not possible.
Lucius: Yeah, it doesn't work that way.
In the forest, it seems Lucius continues running his mouth, likely in an attempt at dealing with his growing anxiety, and in this he is not unlike McKay. But while these things that he says are largely meant to just be Lucius blabbing away, he does manage to say some rather interesting things.
While this had likely not been his first suggestion, the first suggestion that we hear Lucius make is that the two of them hug, Lucius seemingly offering to extend the protection of the shield around Sheppard, which is rather gracious of him -- considering the source. But Sheppard shuts this idea down quickly, seeming very much against it. And it would again be easy to read this as a homophobic comment, as Sheppard not wanting to get physically close to another man even for the purposes of defeating their enemy. Not only does Sheppard as a heterosexual action hero type not want to touch another man, he certainly does not want to hug them like a sissy. There are only a few socially acceptable times for men to hug each other (triumphing in sports, bro getting married to a woman), and it has to be a gruff manly hug with pats on the back at that. Homosocial intimacy is a minefield for straight men to navigate because the line between homosocial and homosexual behaviour is always moving.
But the thing is that Sheppard's issue is not with hugging men, it is with hugging Lucius specifically. We had seen Sheppard recoil from him physically the whole time they have been on this planet, and he has very good reason for this given that Lucius had basically threatened to violate him previously. Sheppard seems to have a history of being victimized sexually and while the perpetrators seem to have been largely women and Sheppard is generally more physically at ease around men, having watched Lucius remove the agency and ignore the consent of everyone he has come to love had left Sheppard more than a little cautious around the guy. And what is curious here is the certainty with which Sheppard says "And it's not possible." He says that it isn't possible like he knows this for a fact. And the only way he would know it for a fact is it that had been something that he had already tried -- with McKay. It is the certainty with which Sheppard makes this statement that is really important here.
Sheppard himself had commented to McKay earlier that he likely wanted "another crack at that shield," having been curious to figure out how it works and what it can do, where the limits of the shield were. McKay was a scientist and so having activated the shield in Hide and Seek (S01E03), it seems the first thing that McKay had thought to do was to test it out. We had joined Sheppard and McKay at the point that they had decided Sheppard should heave him over a railing and drop him down a floor (McKay could easily have jumped himself, this was clearly a project they had undertaken together), Sheppard happily confessing to Weir that he had shot McKay. But even though this had been prefaced by McKay saying that it had not been the first thing they had tried, it does not follow that shooting him had been the first thing they had tried, either. And certainly these two things were not the only things they had tried. And it seems like seeing if the shield could be expanded to cover two people is a thing that they had tried because Sheppard is able to tell Lucius now that it won't work. He knows this for a fact. He has hugged another man trying to do that before. He has hugged McKay. He and McKay had hugged each other. And while it may well have been the first time they had hugged, a personal shield between them keeping them from making actual contact as a ham-fisted metaphor, it had for sure not been the only time the two of them have hugged even if we never get to see it.
Lucius: OK, OK: what if I swung from a clock tower on a long rope right into town?
Sheppard: And?
Lucius: I dunno. That's all I have. I could set myself on fire.
Sheppard: I like that idea.
Lucius starts coming up with increasingly more cartoonish ideas of what he might be able to do to help Sheppard. His first suggestion seems to recall a famous scene from Back to the Future (1985) where Doc Brown is forced to swing on a long rope from a clock tower to connect a cable that might conduct a lightning bolt to the DeLorean to allow Marty McFly to go back to the future.
I had discussed the film in connection with Before I Sleep (S01E15) because Sheppard and Marty have much in common in the way they are portrayed as protagonists. This seemed to be one of Sheppard's favourite films even if McKay had derided it, and it is for sure a film that the two of them might have subsequently watched together. The scene is in homage to the film Safety Last! (1923) where Harold Lloyd hangs from a clock face on a skyscraper, a comedy of errors where a weasely small-time scammer performs a heroic act in spite of himself. What is curious is that Lucius would know about either film, or even know what a clock tower is -- we do not even know how or if various societies keep time in Pegasus. While Back to the Future might have been mentioned in Sheppard's report, it is possible that mission reports were not the only things Lucius had perused during his time in Atlantis, as he then seems to reference other films. He first mentions setting himself on fire, which could be a reference to a number of things, one possibility being the sci-fi film Starman (1984) where the protagonist uses an alien sphere to protect himself and his love interest from an explosive fire. It could also be a reference to the Human Torch of The Fantastic Four, whom Sheppard would associate with McKay in First Strike (S03E20) and which I have suggested is because in his mind, Sheppard genuinely sees McKay like he was Christ Evans' identical twin.
Sheppard tells Lucius that unlike with the hugging, he likes this idea, and while he is obviously flippant, there is at least a part of him that actually wishes Lucius would set himself on fire. He does not actually wish for the man to die but he would not be particularly heartbroken if he did. And while we often hear Sheppard say similar things to McKay, like the "Wish that you would've" he had said in The Return (S03E11), and while Sheppard always means what he tells McKay sarcastically, the difference is that what he hoped McKay would have done was to take up a career where he would not be hurt. But even though he is using a sarcastic tone, he genuinely means what he says to Lucius here too. He does like this idea better than hugging Lucius. But that does not mean he thinks it is a good idea.
Lucius: OK. Um, I could run naked. Oh, I know, I know! What if I got on your shoulders and we have a cloak that they... it's some religious thing... they could be afraid of giants. OK, what if we build a tunnel, OK? We could tunnel... or a boulder -- a huge boulder. I'm camouflaged, I'm protected, now the boulder protects you... or a magnifying glass and some tape...
Sheppard: I have an idea, Lucius.
Lucius: ...some poisoned tape!
The next thing Lucius mentions is running naked, presumably with the intention of distracting the Genii while still wearing the shield. This could also be a reference to a number of things but one interesting possibility is the film Go Naked in the World (1961), which is about a man who returns to San Francisco after leaving the army and tries to assert his own identity against an overbearing father who wants him to marry a girl from their social sphere but who instead falls in love with someone the family summarily rejects only to then lose her tragically. Switching the gender of the love interest, this could basically be Sheppard's backstory, and we may recall that it was in San Francisco that we see Sheppard sitting as he tries to decide what to do with his life at the start of the show. What ever Lucius intends, this does force Sheppard to imagine him naked, to have the mental image seared into his brain, and it is not a pleasant one for him -- and again not because he is homophobic and generally averse to thinking about men naked. And we may note that Sheppard does not actually comment on this idea at all.
The ideas then get even more cartoonish, Lucius suggesting that he gets on Sheppard's shoulders like they were kids trying to sneak into the movie theatre to see adult flicks by hiding under a trench coat. This might be a reference to the film Austin Powers: Gold Member (2002) where Mini-Me takes the bottom position, or the film Hook (1991) where the Lost Boys do this to sneak into Captain Hook's ship, and also done more than once by The Three Stooges. Lucius further suggests that this could be some kind of a religious thing, and next to the wraith worshipers and the people who worshiped Athar this is one of few mentions of people even practicing religion in this galaxy. Lucius seems to imply that stacked on top of each other they would resemble a giant, and this harks back to Beckett's mention of the Highland Giant earlier, a common trope of fairy tales.
It does not seem like Sheppard is warming up on any of these ideas even though he has given up commenting on them, probably trying to think of his own ideas while Lucius is running his mouth. He suggests digging a tunnel, and given that the Genii are known for their underground habitats this seems like an exceptionally poor idea. This idea could be lifted directly from a Merrie Melodies cartoon, and as discussed before, especially Bugs Bunny was in the habit of burrowing tunnels. Lucius then mentions a boulder, and while he suggests that Sheppard hides behind the boulder, this is quite possibly a reference to the iconic scene from Indiana Jones film Raiders of the Lost Ark (1981), and Lucius is not so different from Indy's unfortunate and unscrupulous sidekick at the start of the film. This scene is notorious also for the fact that people seem to hear different things as Indy makes his final quip at his companion ("Adios, Satipo!" "Adios, stupido!"), their interpretation of what is happening altered by their expectations. People frequently actually hear what they are expecting to hear. If Lucius is borrowing from the mission reports he has read, it is also possible that this recalls McKay taking cover behind a boulder in The Defiant One (S01E12) when he had come to save Sheppard, and not only did Sheppard not have to ask him to come, McKay had come even though Sheppard had expressly told him to stay away.
Lucius' final suggestion of bringing a magnifying glass and some tape seems particularly peculiar given that the combination is most often found in connection with disparaging comments about measuring one's manhood, tape required for the measuring in a dick measuring context and the magnifying glass needed to see someone's presumably tiny member. Lucius amends this by suggesting poison tape instead but the suggestion is so absurd that it is difficult to even guess what Lucius might be intending they do with the objects. Magnifying glasses can of course be used to light fires from a distance by concentrating the rays of the sun, resembling the death ray that Archimedes had supposedly invented during the Siege of Syracuse. Again there are a number of things that Lucius could be referencing, and it is an open question of whether he is making actual references to films he had seen while he had been in Atlantis (or even some of their mission reports that likewise might have made references to films), or whether he is simply coming up with absurd ideas on the spot and it had been the writers of the episode that were digging into the trove of movie cliches for things that sound peculiar.
Regardless, Sheppard decides to let Lucius off the hook because while was rambling on, it seems like Sheppard had been able to come up with an idea. And we have seen previously that it is Sheppard who comes up with ideas and McKay is the person who can tell him whether an idea would work or not. And unfortunately McKay is not here right now, Sheppard having to rely on the thing that he often does when bereft of McKay's company to guide him -- the thought What Would McKay Do? And as it turns out, Sheppard decides to do exactly what McKay had done -- one of the first things he had ever watched McKay do.
Although we do not get to see it, Sheppard had presumably helped McKay up off of the floor and they had gone together directly to the control platform to try establishing a connection to Sateda. We now find them back in the meeting room, joined by Caldwell and the others, and it does not seem like anyone has had time or even the inclination for sleeping until they can resolve this situation. But in order to understand what is happening in this scene, we have to again look at what Roon is concurrently experiencing in his homeworld. The interesting thing is that on both sides of this scene with Caldwell, there is a scene in which Ronon is being observed by a camera, which seems to be following him to keep tabs on him. In other words, Ronon is being watched by the bald-headed wraith commander and Ronon attempts to go underground to get away from the camera, to hide from being monitored. We have noted previously how Sheppard and McKay seem to be much more cautious around each other when Caldwell is present or even just in the city, and even now we find them standing basically on the opposite sides of the room from each other, even though they had been very close just moments ago and had to have made physical contact where we did not get to see it.
Weir: We have no choice. We've been unable to dial in to Sateda's stargate.
Teyla: The wraith likely disabled it.
Caldwell: Which means, if the wraith are hunting Ronon, there's a very good chance that there's a hive in orbit. I shouldn't have to remind you the Daedalus has not done well in its last few engagements with wraith hive ships.
McKay: We drop out of hyperspace, we beam him onboard, we get out of there.
Caldwell: You know damn well we can't come out of hyperspace and get close enough to a planet to beam someone off the surface. We'll be detected.
Sheppard seems to be keeping quiet while the others are talking, and it is entirely possible that he is simply unable to say anything at the moment, too overwhelmed by his emotions. The thing to understand is that this is not just about Ronon to him, this is not even just about McKay -- this is also about all the people he has lost in the past, and especially that person he had loved and been unable to save of whom we know nothing yet but who is going to be introduced a few episodes hence. This scene is again followed by some flashbacks from Ronon's past that also hint at what is motivating Sheppard here.
The senior staff seem to be smack in the middle of a conversation when the scene begins, and we do not know what Weir's line about having no choice refers to specifically. But because they are talking to Caldwell, who fortunately seems to have been on Atlantis or in its vicinity at the time, we can assume that Weir is trying to convince Caldwell to let them use the Daedalus in rescuing Ronon. She explains that they had tried dialing the coordinates of Ronon's homeworld. Caldwell is not wrong in issuing caution here, even if his assessment of "the last few times" the Daedalus had gone up against a hive is not entirely fair. The Daedalus is much faster than the hives, so even though it might not be able to easily destroy one, sneaking past one might not be as impossible as he makes it out to be.
But it is also true that Caldwell is responsible for the well-being of his own crew and answers to the SGC and ultimately to the Joint Chiefs of Staff, so it is not for himself that he is arguing here. He represents the military, and given that he had been paralleled with the bald wraith commander -- and the Major with a buzzcut who was also nearly bald had been paralleled with this same wraith earlier (both the Major and the wraith were talking rudely down at McKay and Ronon who were laid down on tables) -- it suggests that the bald wraith especially represents the military to Sheppard in this episode. The war machine is ugly and brutal, it chews up young men and women only to spit them out, often broken shells of who they used to be. The wraith's words to Ronon earlier, "I once fed from the humans of your homeworld. That is where I will watch you die," is symbolic of the patriotic duty of soldiers to lay down their lives for their country. The fact that it is the military that is keeping tabs on Sheppard in this analogy seems fitting. It is the watchful eye of the US military that Sheppard needs to conceal his extracurricular activities from.
Both Weir and Teyla had been trying to argue the case on behalf of Sheppard, as he seems unable to do it himself, but we may note that McKay also speaks for him here, all the while standing what seems to be very stiffly because he is in obvious pain even as he tries not to let it show, offering up a plan of action. It is even more notable in that it is not usually McKay who comes up with ideas and suggestions for what they should do, he is more comfortable in figuring out how to do something. But he wants to find Ronon just as badly as everyone else and although he seems nervous, doing his self-soothing hand thing, he is still brave enough to speak out anyway. We may note that he does not start speaking until he has glanced at Sheppard, before the two of them exchange a look, possibly looking for permission from Sheppard to speak for him. It might also be that by looking at Sheppard's face he is able to tell that Sheppard is not capable of speaking for himself currently and that he has to run interference with regards to Caldwell. But Caldwell shoots down his idea as unworkable and as something that he does not even deem trying out, and we see McKay look at Sheppard again. He seems concerned for Sheppard, and he seems to have good reason for it given how Sheppard finally reacts.
Caldwell: Now, look... you know I wanna help, but I will not put my crew and the only ship that we have in this galaxy at risk for one man.
Sheppard: One man who isn't a member of the US military.
Caldwell: I didn't say that!
Even though Caldwell has been invited to function as the wet blanket here, he does not actually want to be unreasonable, so he tries to explain himself to McKay and starts by prefacing what he says by "Look." We may note that Sheppard looks at McKay on hearing this word, and while he might just be looking at McKay because McKay had been looking at him and looking to him for some direction of what they are supposed to do here, we have noted previously that Sheppard seems to have developed a Pavlovian response to this word that McKay has very often used in situations of life and death, and so when ever Sheppard hears the word, he needs to see McKay's face. But although he looks at McKay, Sheppard is also listening to what Caldwell is actually saying, and we see that he drops his hands as though preparing to throw them.
Sheppard sounds bitter as he finally speaks up, and he sounds bitter in a way that seems to have a lot more backstory to it than is strictly warranted by their current situation. Although Caldwell denies that Sheppard's accusation has merit, he nonetheless seems to have hit the nail on the head and understands enough of the politics of the military apparatus to understand where the rub is for Caldwell, who has to be able to justify his decisions to his own superiors. The US military has a policy of "No man left behind" that goes back at least as far as the French and Indian war of 1754-1763. It means that every person that has entered the service of the US military can be expected to be rescued or retrieved if they are wounded or fallen, exemplifying the respect that the American people and military feel is due to those who have made the ultimate sacrifice. Members of the US military can expect to be rescued by their units and comrades even if it results in loss of life for the rescuers, the phrase having developed into a kind of sacred tenet over the centuries. This is why Sheppard never gives up on trying to find Ford even though in his heart he likely knows that the young soldier had perished.
However, Ronon is not a member of the US military, as Sheppard had pointed out, and hence Caldwell is under no obligation to sacrifice his own crew in retrieving him. This is not the first time that Sheppard has clashed over the topic, as Sgt. Bates had never been able to see Teyla as one of their own, and even Weir had been suspicious of her in the beginning, the fact that Weir had not been able to extend to her or the other Athosians the same courtesy as the members of the expedition having been a sore topic between the two of them. We recall that Sheppard had been upset enough with her to actually yell at her to "Open the damn gate!" in Suspicion (S01E03). But as mentioned, this is not just about Ronon to Sheppard. Teyla is also not a part of the US military, and even though McKay is contracting for the military, as a Canadian citizen he too is not under the aegis of this policy. If push came to shove, Caldwell would be under no obligation to retrieve McKay either, and that is unacceptable to Sheppard.
Thinking about the unfairness of the policy seems to be making Sheppard so angry that he is actually shaking with it. Weir looks at Sheppard with concern because she has never heard him sound like this before -- none of them have. And notice again how Sheppard seems to smile here even though he is about as unhappy as he has ever been. It seems like smiling is something that Sheppard does before he strikes, about to lash out verbally here. It seems like Sheppard actually tries to calm himself down by looking away from Caldwell but he just feels too strongly about this to be able to keep it in a moment longer.
Sheppard: He's a member of my team, and he deserves the same respect as anyone on this expedition.
Weir: We don't leave our people out there, Colonel, not if there's any chance.
Caldwell: Don't preach to me about leaving people behind, Doctor Weir.
Sheppard walks up to Caldwell and gets right in his face, punctuating what he is saying with his finger, and given that Caldwell is the superior officer, even though Sheppard is not serving under him, this is skirting very close to insubordination. Article 90 of The Uniform Code of Military Justice states that assault consists of threat or offering of violence against the officer, striking the officer, or brandishing a weapon in a threatening manner against the officer. What is more, this seems to be the very article that Sheppard had disobeyed when he had received his black mark in Afghanistan, assault and disobeying a superior officer falling under the same article. We know from Rising (S01E01) that he had received his black mark from disobeying a direct order not to cross enemy lines to rescue someone, and in Phantoms (S03E09) we finally see the person Sheppard had tried to rescue, but in this episode, through Ronon's flashbacks, we learn more about the circumstances that had led to these events.
It is not an accident that Sheppard gets in Caldwell's face and brings himself very close to violating the same article here again, because what had happened then is at the back of his head and the forefront of his mind the whole time here. Note the way McKay and Beckett exchange a glance behind the two of them, probably wondering what they are going to do if this is going to come to blows. This is not about Ronon, this is not (entirely) about McKay, this is not about Teyla, who Sheppard glances at just before launching himself at Caldwell -- this is about "the one that got away." This is about the man he had been unable to save. This is about Captain Holland.
And given that it is the US military's "No man left behind" policy that seems to be triggering to him, and the fact that he had been expressly forbidden from crossing enemy lines to rescue Holland, it begs the question of whether "Dutch" was actually not from the United States. We know very little about the man and he certainly has a North American accent, but the military contingent in Afghanistan was actually an international coalition. Holland obviously was not wearing insignia that would have given away his nationality while on a mission, so I am just going to go ahead and raise the question of whether he had, in fact, been Canadian. If he had been US military, it would be strange that they not only would not have attempted a rescue but had expressly forbidden Sheppard from going to get him. And this would explain Sheppard's bitterness here, would explain his strong feelings about this particular topic.
Another thing that might be upsetting Sheppard here is what had happened in The Long Goodbye (S02E16), not too long ago. Not only does Sheppard glance at Teyla before getting in Caldwell's face but McKay exchanges a glance with Teyla too. It might be that both of them are worried about Sheppard, to be sure, but it might also be that both of them are remembering what had happened when Caldwell had assumed command of the operation even though McKay had felt like it should have gone to him as the senior most civilian member of the staff at the time. We may recall that Caldwell had refused to give Teyla an order when Phoebus had made the ultimatum of Teyla either shooting Sheppard or her letting a bunch of other people die. Instead of giving the order and taking the responsibility for what would happen, like Caldwell would have been duty-bound to do if Teyla had been Earth military, Caldwell had instead told her "I'm not gonna tell you what to do," skirting his responsibility.
Some people had undoubtedly interpreted him as being compassionate or like he was being supportive of Teyla in what ever she would decide to do in the situation, but Sheppard certainly and McKay possibly both understood what had actually happened there. Even though Caldwell had taken command of the city, he did not see Teyla as one of his men. Teyla was neither under his command nor under his protection. Sheppard might not have said anything to Caldwell at the time because he was wanting to keep a low profile and dealing with the report of Weir having kissed him was already difficult enough, he did not need the attention from the SGC. But what he is telling Caldwell here is something that he could also have told him back then: She's a member of my team, and she deserves the same respect as anyone on this expedition.
Weir may not understand the entire subtext of Caldwell and Sheppard's exchange here, but she is likely feeling guilty enough about her own past dealings with the Athosians that she feels the need to take a stand by Sheppard in this. They had taken Ronon in and he has more than proved his loyalty to them. Just like Ronon feels like he owes a debt of gratitude to Sheppard, so Weir feels that they owe a debt of gratitude to Ronon and her sense of justice is telling her that it is the right thing to do to try to save the man. If this episode originally followed The Real World (S03E06), like speculated previously, Weir may also feel like she owes a debt of gratitude to Sheppard at this time. But Weir and Sheppard's motivations are not the same here. She is doing this because she thinks that it is the right thing to do, for Sheppard this is more than personal. He is not just speaking up for Ronon, or Teyla, or even McKay. He is speaking up for the phantoms of his past. He needs to make this right even though he is too late to make it right for Holland. Sheppard is now what he has been accused of being by so many of his superiors, entirely compromised by his feelings.
Caldwell: I'm just saying it's a very bad risk/reward situation.
Sheppard: Fine. Then just get us close. We'll take a cloaked jumper the rest of the way.
Beckett: I'll go with them, remove the tracking device before we get back on board.
And yet, even though Caldwell is represented by an actual ogre in this episode, he is not a bad man. He is not unreasonable and he does not wish ill on Ronon, even if he is not willing to sacrifice his own men to save him. He tries to make Sheppard understand it from his point of view as the captain of their only space ship in this galaxy and currently their only means of travelling from the Milky Way to the Pegasus. He bottomlines it for Sheppard, and because Caldwell seems to somewhat relent, or at least is not looking for a fight with him, Sheppard starts bargaining instead.
They do not have time to be talking about this for a really long time, so once more it is Sheppard that comes up with an idea that they might be able to implement, especially with Beckett also jumping in to assure Caldwell that they will be able to get Ronon out without the wraith being able to follow them. What is interesting here is that once more Sheppard seems to use "we" in the sense of himself and McKay specifically, even though this situation as such does not occasion that kind of sentiment. Between saying "get us close" and "We'll take," his eyes go to McKay, likely entirely subconsciously. He just seems unable to think of the word "we" without looking at McKay, because to him "we" is always the two of them. He will take a cloaked jumper with McKay and the others can tag along if they want to, but Sheppard is speaking for the two of them here. He does not need to ask McKay if he wants to come along even though he probably should have stayed back. Neither one of them wants to be separated from the other.
Sheppard: We'll be out of there before the wraith even know what happened.
Caldwell: I won't bail you out if you get in trouble.
Sheppard: You say that as if we're always getting in trouble!
We may have seen an echo of Sheppard's argument with his father in the beginning of the episode, a fight that had been so severe that it had caused Sheppard to walk out on his family, to feel like he has no family left on Earth and that he had been disowned by his father. But while Caldwell is probably not quite old enough to be Sheppard's father, there is certainly a dynamic to their exchange here that is like between a father and a son. A son wants to borrow his father's car and promises to have it back before he even notices it is gone, and the father agreeing to lend it only under duress and warning the son that he is not going to be responsible if he gets himself or others hurt while driving.
But at the same time, "I won't bail you out" may actually have been something that Sheppard's father had either explicitly told him, and even if he had never said the actual words to him, it must have been what he lived by. Sheppard may have made the decision to join the military but if he got in trouble, his father would not use his wealth and influence to get Sheppard out of trouble. And Sheppard had found himself in trouble, and while we do not know the details of their altercation, Ronon's earlier pleading of "Don't make them pay for my mistakes" might have been something that Sheppard had similarly begged of his father when Sheppard could have used his father's help and influence. And what Sheppard does not know is that his father had helped him. Sheppard could easily have wound up a hollow shell of a man like his counterpart in Vegas (S05E19), but even if he never found out about it, his father had intervened on his behalf. The military seemed important to his son and what ever he had done to make the dishonourable discharge dropped, Sheppard had then been able to continue serving in the military, flying choppers in the most remote part of his world.
Sheppard's quip at the end, which he throws in just before walking out the door, is intended to lighten the mood both for himself and others. Caldwell may or may not feel like Sheppard and his merry band of misfits are always getting in trouble, and that he is always having to bail them out -- something that he had done successfully in The Siege (S02E01), Trinity (S02E06) and Inferno (S02E19), and probably felt like he had done in Conversion (S02E08), Aurora (S02E09), The Hive (S02E11) and The Long Goodbye (S02E16). His warning is not entirely unfounded. But it is also true that Sheppard had bailed him out in The Intruder (S02E02), Critical Mass (S02E13) and No Man's Land (S03E01). We will disregard Allies (S02E20) in this because even though Sheppard claimed to go out to help the Daedalus, that did not seem to be his actual intention at the time. Caldwell has a point but Sheppard also has a reason to feel like he is being unfair and exaggerating their tendency to find themselves in trouble on a weekly basis.
What is really interesting here is the expression Sheppard makes just as he takes his leave from Caldwell. He delivers his line like he is affronted, which is partially a performance but also what he really feels. But then he bends his head, lifts the inner corners of his eyebrows while opening his eyes wide in an expression of innocence, very briefly giving Caldwell the face of an angel that he must have used in his youth when he had been doing things he should not have done, when he had been caught doing something naughty, a face that would have made nannies and tutors and older female relatives forget all and everything because he looks like such a sweet little boy. The fact that he is able to put on this face at will even though it is not even in the ambit of what he is actually feeling here tells us that he is practiced in manipulating people, in performing roles, in making people see what they want to see. This is very much an example of his weaponized use of his charm. And let us not downplay the fact that Sheppard actually manages to talk Caldwell into doing something that he was disinclined to do. Sheppard was able to sway him to see things his way. Sheppard was able to push Caldwell into doing what he wanted him to do. Sheppard seems to feel very strongly about this.
This scene, Sheppard getting in Caldwell's face and then making a grand exit is paralleled by Ronon on Sateda. He first approaches the camera that is following him and spits "You're going to have to do better than that!" at it before shooting it, and we see the bald-headed wraith commander seething with rage. He then flicks the pin off of a grenade of some kind, tossing it behind him and walking away without even looking at the ensuing explosion, cool as you please. Both the angry pointing at a bald guy and walking away from the scene without looking back parallel what Sheppard had just done on Atlantis, and whether Caldwell had felt like growling too, we do not know. Important here is that the scene for Ronon was preceded by him walking through the corpses of his fallen comrades and the phantoms of his memories of the men who had served under him and whom he had led to their deaths. Armed with these memories, he had been able to take out the wraiths hunting for him. And Sheppard seemed to find the wherewithal to stand up to Caldwell here armed with his own memories of all the people he has lost on the battle field. There is a radio broadcast in Ronon's memories that tells us "Sateda will not bow to invaders." For what it is worth, United States of America is an anagram for Satedar metafictions.
In hyperspace, on the Daedalus and on their way toward Sateda, Teyla joins Sheppard in the commissary where he seems to be finishing what is likely his breakfast, alone -- and as noted before, it seems like breakfast is the one meal of the day that Sheppard and McKay rarely get to enjoy with each other. The two of them have a conversation that teaches us a lot about Sheppard and which I have quoted multiple times because it is so central to his character. But in order to understand again the undercurrents of their exchange, we are shown a long stretch of backstory for Ronon that informs how Sheppard is feeling here, why he is as vulnerable and raw as he seems. In his memories, we see Ronon walk through a tunnel littered with the corpses of his dead friends and fallen comrades, the ghosts of his past, while in the present we see him fighting off his demons that are threatening to overpower him. As Sheppard is joined by Teyla, he is doing both of these things figuratively, even though he appears easy as you please to begin with.
Sheppard: Hey.
Teyla: Am I disturbing you?
Sheppard: No.
Teyla seems to have sought Sheppard out with the intention of exchanging a few words with him about the situation, and if one was uncharitable, we might call it ambushing Sheppard while he is finishing his meal. The commissary seems otherwise empty, two of the other occupants leaving just as Teyla enters, which suggests that Sheppard was either eating at an unorthodox hour or that he had lingered there after others had finished their meals. What we need to note at the off-set is that this scene seems to coincide with the following scene where McKay and Beckett have a conversation of their own, both Sheppard and McKay having heart-to-heart talks with their respective best friends. While we see the entire interaction between Sheppard and Teyla here, we catch only the tail-end of the time that McKay spends with Beckett. Also, it seems like Sheppard's tray has a few slices of tangerine on it that he has chosen not to eat, and it looks like he has left the compartment for dessert untouched. Make of that what you will.
Sheppard is doing something on a Personal Digital Assistant as Teyla joins him, a palm device of some kind that was probably hi-tech at the time, and we can be fairly certain that the reason Sheppard even has one, let alone that he would have known which one to get, is McKay. We had seen Sheppard reading (and writing) something off of a palm device at the end of The Long Goodbye (S02E16), where he seemed to be communicating with someone on it while laid down on a hospital bed, smiling to himself at what ever this person had written to him. Here, he also seems to be either reading or looking at something on the screen, and he pushes a few buttons before putting the device away, which means that he either closed a programme or typed "brb" before shutting it off, knowing that it would be rude for him to continue fiddling with the device when one of his team members clearly wanted to engage him in conversation. Sheppard tells Teyla that she is not disturbing him but that does not mean that he had not been in the middle of something when she walked in, or even that he is telling her the truth. Also, even if Sheppard was being truthful about Teyla not bothering him at the moment, by the end of the scene he is more than a little disturbed.
In Ronon's flashback, we see a fight between him and his "close enough" Malena,* which suggests that Sheppard and Holland also had a fight before his fatal mission. This would have made Sheppard feel even more guilty afterward because, whether or not he had asked him not to go, Sheppard thinks that he would have been able to stop Holland if he had truly wanted it. He could have ordered him not to go but he hadn't, he had decided to honour Holland's autonomy instead and this decision not to tell someone he loved what to do had cost them their lives. In Sheppard's world this was tantamount to having caused their death. He might as well have pulled the trigger himself. But loving someone meant letting them go when they needed to go, and this has everything to do with what happens later with him pushing McKay toward Keller after the lesson Sheppard learns in Miller's Crossing (S04E09).
In his flashback, Ronon is dressed in civilian clothes and has the following exchange with his loves after returning from a combat mission:
Dex: No one that stays here is going to survive.
Malena: Then why are you staying?
Dex: I have no choice.
Malena: Yes, you do. You believe in this fight! You know that they'll eventually find us, no matter where we go. Our only hope is to show them that we're not worth the effort, to go feed on some other planet that won't fight back as hard as we will. Ronon! You can't run forever.
We do not know the particulars of the events that had led to Holland taking on the mission that claimed his life. In Rising (S01E01), Weir says that Sheppard had received his black mark in Afghanistan trying to save the lives of three servicemen and disobeying direct orders in doing it. In the parallel world of Vegas (S05E19), his record stated that he had been a helicopter pilot in Afghanistan that was dishonourably discharged for disobeying orders trying to rescue a field medic trapped behind enemy lines, and that his attempted rescue had further killed four American soldiers along with eight civilians. Now, there is an obvious discrepancy between these reports, but note that the description in Vegas of him trying to rescue a field medic trapped behind enemy lines corresponds with what we actually see in Phantoms (S03E09), regardless of the gender of the field medic, much better than what his record stated in our world. This suggests that his record in our world had been altered. His impending dishonourable discharge, which he clearly believed he would get as he asked Holland to visit him in the Leavenworth prison afterward, had been turned into a black mark. His record, in our world, does not show what had actually happened in Afghanistan. And what is more, he may not even know this himself. He may have no idea that his father had intervened here.
But the thing about falling in love on the battle field, as Sheppard had done, is that the person he had grown to care about was in ever-present danger. As glad as Sheppard had been to find someone that unlocked something deep within him, had healed some parts of him that he had not even known needed healing, who had changed the course of the rest of his life -- the circumstances of their relationship were doomed from the start. The odds were stacked up against them on an active warzone and so Sheppard would have wanted to send the man that he had fallen in love with away from there, even if he believed that he could never leave himself. Knowing that Holland would be safe was enough, it would have to be enough. Only, being that he was a medic Holland could not abandon all the people that needed his help either, and this must have become a point of contention between them.
The other point of contention may have been that they were forced to hide their relationship. If Holland had been Canadian, as I have speculated, then he would have been able to serve openly as a gay man, Canadian Armed Forces having repealed the order banning gay people from serving in 1992. What Malena tells Ronon is something that a gay man in the service could easily have said to his closeted lover: "You believe in this fight [for gay rights]! You know that they'll eventually find us, no matter where we go. Our only hope is to show them that we're not worth the effort, to go pick on some other people that won't fight back as hard as we will." Because Sheppard was in a more precarious position because of the US DADT policy, he would have been much more reluctant to go public, to be open about their relationship, to jeopardize his career just to make a statement, and Sheppard may have thought and even said many things that would not have mattered a damn thing after the man that he loved had died. Malena telling Ronon that he can't run forever is ironic given that he had subsequently been made into a Runner, but Holland may easily have told Sheppard the same thing. Like Ronon, Sheppard has spent most of his life running, and most of it he has been trying to run from himself. What he is doing right here, staying in this table to try to have this conversation with Teyla, this is him trying not to run.
Sheppard: What's up?
Teyla: I just wanted to thank you.
Sheppard: For what?
Teyla: For going after Ronon this way.
Sheppard: Did you think we wouldn't?
Sheppard's "Did you think we wouldn't?" and McKay's subsequent "What makes you think I wouldn't?" to Beckett clearly connect these two scenes, we are meant to see them as a matching set. In this instance Sheppard's "we" seems to refer to himself and Teyla, to his entire team, to the people of Atlantis, and the people of Earth in general -- but like always, it is first and foremost himself and McKay. Teyla may be thanking Sheppard in particular with her "you," but Sheppard chooses to understand it as meaning himself and McKay, and he speaks for the both of them as he responds, which would feel even more natural for him to do if he had just been chatting with McKay who had not been having breakfast with him on account of currently undergoing a check-up with his primary care Physician and best friend elsewhere -- knowing that he could not sit down to eat with him even if he had wanted to anyway. But giving Sheppard a device that he can use to communicate with him even when he is not physically present seems "like a McKay sort of thing" to do.
Sheppard is genuine in trying to communicate to Teyla that no thanks are necessary for them doing the right thing. What is more, he would rather have avoided this conversation, even though he recognizes that this is something that Teyla needs to get off her chest. He knows that it is his responsibility as team leader to be there for the members of his team but he is not good at this and he had been hoping that they might avoid this. But theirs is not an unspoken bond that goes deeper than words, my friend, deeper than words, and so he submits to his fate and to having this conversation having actual words, even though it is anything but easy for him. That is one of the reasons to show Sheppard struggling through having this conversation. He and Teyla need to talk things out where he and McKay do not. Sheppard and McKay have a mutual understanding, the uncanny and unsettling ability to read the other's thoughts by looking at their face.
Sheppard and Teyla are friends and they have had intimate conversations before, particularly in Hot Zone (S01E13) and Letters from Pegasus (S02E17). The latter of which is especially pertinent to their conversation here because they had discussed the topic of home and family and friends who are like family, which is precisely what this conversation and this entire episode are about. Quoting from what I had written then:
Sheppard also considers the people he has found on Atlantis as his family. I've discussed previously why he places McKay ("even Rodney") in the final position before (he attempts to mitigate the emotional impact by saying the most important thing last). But here, there is also an actual categorical difference between McKay and the others he mentions.
Yes, he considers all of them family but out of them, McKay is the only one of them who belongs to that second family one forms when one leaves one's birth family or family of origin to make a new family with a partner. The others he mentions are his "found family," a concept with which many non-heterosexual people are familiar with. A found family or family of choice is "a group of people without any blood relation that supports and cares for someone the same way family members would." They are that to him. McKay is his conjugal family, and there is a whole other set of responsibilities (and also privileges) that comes with that. And Sheppard also emphasized the fact his family are not his friends, they are different from that.
Sheppard does not feel like he has a family back on Earth. As far as he is concerned, he has been disowned by his father and abandoned by his brother. He is clearly uncomfortable discussing the topic with Teyla. He does, however, consider Atlantis his home. Months ago, in The Storm (S01E09) he told Teyla: "Well, maybe in time this place will start to begin to feel like home." And later on, he confesses to the same person that he thinks of these people as his family. Sheppard and McKay feel exactly the same way about their situation. Atlantis is home and the people therein are family. They are family to each other.
And it's also interesting that the difference between a family and a dear friend is emphasized in this episode. Many people find it strange that McKay calls Beckett his best friend later on [in Sunday (S03E17)]. But the thing is, McKay and Sheppard were never friends. They have never been friends. They are family but, in spite of just having an entire episode about brotherhood, they are not brothers, they are not cousins, they are not uncles or parents or nephews to one another. They are family but in a very different way than they are family to the others.
This was true of the two of them already toward the end of the first season, and Sheppard and McKay have only grown more close since then. Comparing this scene, this intimate exchange between Sheppard and Teyla that some people undoubtedly interpret in a romantic context, with the exchange between Sheppard and Mckay at the end of the episode, it is easy to see with whom Sheppard is at home. At the end of the day, when all is said and done, his home is with McKay.
Teyla: He is an outsider.
Sheppard: Not to me.
Teyla: I have often felt like an outsider among your people.
Sheppard: Well, maybe at first, but... Well, you know I've always trusted you.
Teyla: Yes. You, and Doctor Weir have been very accepting, but this has shown me how far you would go, even for someone who is not from your world.
Sheppard seems to be putting extra effort to appear casual about this because he wants Teyla to feel like it is obvious to him that they would do this, that he thinks of both Ronon and her as one of them. He wants her to get the impression that he feels "Well, duh!" about it, and the fact that he seems to be putting so much effort into this performance, into making Teyla feel like she belongs, is telling. Sheppard knows the importance of good old team spirit. But you can tell that he is feeling defensive by how he places his hands around his tray just as soon as he puts his cup down, as though subconsciously protecting it from Teyla. He seems to need an emotional barrier between them.
Sheppard himself has felt like an outsider probably for most of his life -- he has been an outsider within his own family, thinking himself as the black sheep, a literal outcast. He has been an outsider in the military because he comes from a social class that does not usually rise through the ranks but goes directly into officer training, that goes to West Point instead of bleeding on the battle field with the guys. He is a man who loves and desires other men in a society that ostracizes acting on these impulses, which is why he has tried to create an environment for the people under his command where they might feel free to love whom ever they please. It is important to him that the people he cares about feel like they belong because, for such a large part of his own life, he felt like he did not belong anywhere. That is why coming to Atlantis, the city of his ancestors that had welcomed him with open arms had been so transformative to him. That is why McKay accepting him even when he had actively tried to push him away following The Eye (S01E11), when he had been at his thorniest, had given him the strength to try again, to let himself fall in love.
Teyla acknowledges that Sheppard has always been accepting of her but she then also mentions Weir, and it is actually possible that she does not know that some of the worst fights between Sheppard and Weir had been over her choosing Stg. Bates as her head of security and listening to his suspicions of Teyla. We had seen Sgt. Bates air his suspicions of Teyla in Suspicion (S01E04), The Gift (S01E18) and The Siege (S01E19), and especially before Sheppard had forced Bates to side with his call in Hot Zone (S01E13) Weir seemed to trust the judgement of the man that she had put in charge of security personally. It could be that she thinks that Weir had trusted her from the beginning because when Weir had interviewed the Athosians, she had not asked to interview Teyla and had implied to her that it was because she trusted her when in their internal discussions Sheppard had to basically bully her into treating her as a member of his team. In Suspicion, hey had the following exchange:
Weir: Teyla… I wasn't expecting you.
Teyla: I was surprised to be left off your list.
Weir: I didn't feel it was necessary in your case.
Teyla: On the contrary. You should have spoken to me first.
Weir: You're right. I should have.
It is easy to see why Teyla would come under the impression that Weir had trusted her implicitly when what she had actually been doing was to maintain a fraught peace with Sheppard who seemed to make trusting Teyla the linchpin of his continued cooperation with her. What is more curious is why she does not name McKay here because he never seemed suspicious of her and was offended on her behalf when Bates had forced him to search through her belongings. Perhaps it is, as McKay himself suggests momentarily, that people have real trouble seeing him for who he is sometimes.
Sheppard: Look, Teyla. I'm not really good at... Actually, I'm... I'm terrible at expressing... I don't know what you'd call it...
Teyla expresses her gratitude and appreciation for what Sheppard had done openly and honestly, and Sheppard clearly does not know what to say to that. But because Teyla keeps looking at her expectantly with an encouraging expression, a friendly and welcoming smile on her face, Sheppard recognizes that she needs something from him, he needs to say something in return. Do not miss the fact that Sheppard begins the difficult task of muddling through baring some of himself to a member of his team who seems to be in need of reassurance with the word "Look," perhaps trying once more to use the "What would McKay do?" question to help him out of a sticky situation. And while many people do not recognize it, McKay is actually emotionally much more open than Sheppard, he is brave enough to bare his soul to others without fear of judgement. McKay's presence actually makes it easier for Sheppard to express emotion, as seen at the end of Letters from Pegasus where he seemed to be looking out to the side of the camera for that one other person who had no family back on Earth for strength as he recorded his video message to Col. Sumner's family.
But it does not seem to help Sheppard find the words any easier here. One thing we have to acknowledge about this scene is that as Sheppard struggles to find the words and Teyla keeps suggesting expressions to him, they do not seem to be precisely what he was looking for. We had seen in the previous episode that Sheppard is persnickety about words and their connotations, and so far McKay has been the only one who has managed to feed him words that he accepts. There is a comedic beat to Teyla suggesting "feelings" here, but likely Sheppard was looking for something more nuanced than that. He is not really good at the emotional intelligence side of military leadership. He is not good at managing the emotional needs of people under his command. He is not good at offering comfort or verbalizing his feelings. He is terrible at expressing compassion and comfort. He is not a very sensitive man. To interpret him meaning that he is merely bad at talking about his feelings is to miss his point. He is bad at expressing feelings and he would very much like the avoid having this conversation but it is much more that he has spent so much of his life hiding who he is that he finds it painful to have to bare himself to others, to show something of the real person underneath the façades. He had never even really set out to show McKay who he is -- McKay had just been able to see through him in a way that was almost preternatural.
Teyla: Feelings?
Sheppard: Yeah, sure, OK. The point is, I don't really have good...
Teyla: Social skills.
Sheppard: Well, that is why I enjoyed flying choppers in the most remote part of my world before all this craziness happened.
This exchange is important because Sheppard verbalizes something about himself that we have known for a long time and that is one of his core characteristics. But we should also note that he does not precisely agree with the descriptions that Teyla is offering to him as he tries to come out with what he wants to say and to find words for what he means, actually seeming borderline offended that she would think this way about him. He is willing to go along with her assessment of his character just to get through what he wanted to communicate to her but it is obvious that they do not have the kind of accord that Sheppard and McKay have, they do not have the kind of unspoken bond that goes deeper than words that he mentions in the next scene. Also, let us just note for the record that what Sheppard does here, sharing a piece of personal information in an attempt to bond with someone, is like a McKay sort of thing to do.
One might think that the fact that they are having this heart-to-heart and that Sheppard is having difficulty finding words that it would imply their connection goes deeper than words but it is actually the opposite -- they both require words but Sheppard is having a hard time finding the right ones, and Teyla keeps offering the wrong ones. It is rather obvious that Sheppard had not meant to say "feelings," and he just decides to roll with "social skills" even though he was going for something different. It was clearly intended to be plural, so it might have been something to the effect of "good ways of expressing myself," "good words to express what I feel," "good experiences in bearing myself like this." Even though Sheppard may have some wants in the social skills department and in fact his entire team are somewhat stunted in this regard, that is still clearly not what he had intended to say and he seems a little hurt that that is the first conclusion she would jump to.
Even flying choppers in the most remote part of his world does actually require some social skills. He might actually think that he does have good social skills because it has always been easy for him to charm people and to convince them to see things his way, to navigate social situations using different masks and personas without having to bare himself to anyone. Good social skills obviously require much more than just surviving social environments and there are things about being intimate with other people that Sheppard and McKay have only recently started learning with each other. But that was not his point. His point is that he may not be good at this but he still wants to let Teyla know that he appreciates her and that he is trying very hard to be the leader she needs him to be.
Sheppard: But you should know, I don't have...
Teyla: Friends?
Sheppard: No, I have friends! You, Elizabeth, Ronon... Carson -- even Rodney -- are the closest thing I have to a...
Teyla: A family?
The important thing to note here is that Sheppard had intended to say that he does not have a lot in the way of family initially. He is uncertain and searching for words here because it is complicated and he does not want to lie to Teyla. Technically he does have family on Earth but practically he feels like he has none because he is under the impression that his father had disowned him and his brother had abandoned him and he had divorced his ex-wife. He had a birth family and he had a conjugal family once but he had walked away from both of them. But to put all of this into words that would not reveal too much, would give Teyla the essence of what he meant to say and that would not involve lying to her seemed to be more than a little difficult and so he does not quite know what to say, or how to say that he has come to think of her and the others as his family instead of his blood relatives back Earth. But we know he was not intending to say "I don't have friends," because he takes immediate offence at Teyla saying it, for even thinking that he has no friends. Sheppard has friends.
And then he starts listing his friends. Sheppard starts listing the friends he has made in Atlantis because most of his friends back on Earth are dead. Back in Home (S01E09), Teyla had seen a whole house full of people from Sheppard's past including some of his close friends, so Sheppard seems nettled that she would even think that. But he starts listing his friends, and we may note that he begins with Teyla herself, considering her his best friend here. Teyla, Elizabeth, Ronon, Carson -- they are all whom Sheppard considers his friends now. But because he had actually been thinking of family to begin with, he switches gears in the middle of listing these people and starts naming friends he considers family instead. All of the people, they are his friends whom he has grown close enough to consider them his family, his found family on Atlantis. They are like a sister (Teyla), a mother or aunt (Weir), a brother (Ronon) and a father or uncle (Beckett) to him. And the reason Sheppard says "even Rodney" is not because he is not close with McKay like he is with the others. It is not because he does not consider McKay his family. It is not because he somehow thinks of McKay as the runt of the litter or that he cannot for some reason admit that he does like McKay because he is too cool for school like that. It is not that he considers McKay the red-headed step-child of his family. It is because he does not consider McKay his friend. That is the rub.
I have noted before that Sheppard has this tendency to slip important things under the radar as though he could protect them from cruel fate if he does not admit how important they are to him. Sheppard thinks that his love is literally lethal and so the more he loves something, the more he has to try to convince the world that he does not care about them at all. If he can trick people into thinking that he does not care about the things that he cares about, maybe fate will leave them alone. That is why he tacks McKay on at the end, and we can see how he speeds up what he is saying here, he is trying to say McKay's name so fast that he gives Teyla precious little time to stop to think about what he is saying here, he soldiers on as though he had not even mentioned McKay, and many people take this to mean that he cares about McKay the least when the truth is the complete opposite.
It is speaking McKay's name that makes Sheppard think of family and to switch gears from listing friends to listing people he considers family, and it is mentioning McKay that makes him tear up, that overwhelms him and makes him choke up with emotion here. McKay is the most important person in his life bar none. But McKay is not his friend. McKay is not his birth family. McKay is not like a brother to him. But McKay is also someone that he is not allowed to marry and start a conjugal family with like he would very much like to. McKay is his "close enough," but because they are not allowed to be to each other what they are in their hearts, he does not know what category to place him in. McKay is the only person he mentions that he could and would make his actual literal family -- if the laws allowed it. It is further Sheppard's career that keeps them from being able to marry, as the McKay in Vegas is married, being that gay marriage was legal in Canada, and he sure as heck was not married to Keller. It is also entirely possible that in spite of the two of them co-habiting at this time that they have never had the "What are we?" conversation. He knows that they are not friends like he is with the others, and he knows that McKay is not family to him in the same way as the others. Note that he does not look at Teyla as he says this but looks to the side, more than likely toward the direction that he knows McKay currently is. McKay is more than family to him. McKay has become so close to him as to make up a part of him, and if he were to lose McKay it would be like losing a limb, only worse. He would lose half of his soul.
Sheppard: I'd do anything, for any one of you. If I had to give up my life the way Ronon was going to, I would.
Teyla: Thank you. For everything you meant to say.
Sheppard is finally able to make himself say what he had intended to say, and it is anything but easy for him. He needs Teyla to know this but he would much rather have hoped that it goes without saying. And we have to appreciate the fact that even though many people think that Sheppard has some kind of a death wish or a saviour complex -- Caldwell included in this -- it is not just for anyone that Sheppard actually would lay down his life. He is not like Col. Sumner who was able to lay down his life for an ideal, for an abstraction. Sheppard would do anything for the people he cares about, for the people he loves, but he does not want to die. Especially now that he has found love, he very much wants to keep living. But while he says that he would do anything for any one of them, and he probably would give up his life for them, we are shown again and again that he would go above and beyond for McKay. With McKay, he actually means anything. He would literally let every single human being including future generations and the entire human race die just so McKay could be happy for a moment, and that's a thing that happens on the show. He would not do that for the others. While he might easily be able to give up his own life he would not let McKay die to save any of the others but he would sacrifice all of them to save McKay. That is the difference.
The question of the original sequence of the episodes comes in here, as well. As it is, Sheppard and Teyla have this conversation before Sheppard has to make the choice to give up his life for the others in Progeny (S03E05), and the fact that it is just a scenario constructed by the replicators does not change the fact that he makes the choice to do that. As it is, he makes the choice now after having experienced Ronon doing the same for them, which makes it come across as reciprocity. But originally, his sacrifice in the mental scenario that no one else even knows about and him risking his own life to save Weir at the end of The Real World (S03E06) had come before this conversation. Sheppard knew that he would do what Ronon had done because he had already done it, he had experienced it recently. Giving up his life for the people he loves had been the easiest choice in the world.
Sheppard pats Teyla's hand awkwardly and walks way from her after getting this off his chest, and we may note that he does not turn to look behind him at her as he leaves because he has no need to get that "one last look" at her, because he is not interested in her romantically and never has been. In Search and Rescue (S05E01), as Sheppard is dying from internal bleeding and is under the belief that his actions had killed McKay, he has a hallucination about two members of his original team: Teyla and Ford. McKay is conspicuously absent from this hallucination. In this hallucination, that I have discussed many times is based on an actual memory, Sheppard is having dinner alone together with Teyla. They are having wine in candle light, the whole romantic nine yards of it, and Teyla tells Sheppard that she has always cherished "these times when it is just you and me," which is something that McKay had told him in Harmony (S04E14) while the two of them had been having wine. We are shown that this is not true in the episode itself, where Sheppard and Teyla are both awkward as they are forced to spend time alone together in the hospital at the end of the episode, even though both of them even have a distraction they can hide behind. It is actually connected to this scene in that Sheppard seems to be playing a game on his handheld device just as he does here -- or doing some work, or communicating with someone else. We never do find out what he does with them but we can be fairly sure that the reason he has such devices is McKay.
It was established already in Conversion (S02E08) that Sheppard and Teyla have no romantic interest in each other, they are "friends, nothing more." Here we are further shown why they never could be in an intimate relationship with each other. Teyla needs things that Sheppard is unable to give without destroying himself. The effects of this conversation are devastating to him. The scene is framed by Ronon attempting to outrun an explosion that destroys an entire building and picking himself up injured from the rubble afterwards. This reflects the effect that this heartfelt conversation with Teyla has on Sheppard internally. Having to bear himself open like this is not just difficult for Sheppard, is tears at the very fabric of his defensive mechanisms. McKay is patient with him. McKay does not make demands on Sheppard to express let alone verbalize his feelings, and he will wait 40,000 years for Sheppard to be ready if that is what it takes. While it took McKay almost dying in Tao of Rodney (S03E14) for Sheppard to almost confess his love to him, McKay had never pushed him to do it and he was grateful to get confirmation even in as convoluted a way as he does.
As mentioned, the scene just before this one featured Ronon combating a bunch of wraith, and just as soon as he thought he had gotten on top of the situation, one of them had triggered a self-destruct sequence that blew up the entire building and Ronon was running for his life to get away from the devastating explosion. Following this scene, we find Ronon digging himself up from the rubble clearly badly injured by the falling debris. And these events are framing this exchange between Sheppard and Teyla because the effects are similar to him emotionally as the building exploding and falling on top of Ronon had been to him physically. That is how difficult baring himself emotionally is for Sheppard. This was not a healing experience for Sheppard, even if for Teyla it had been something that she sorely needed from him, and that is why he had soldiered through the conversation. He could see that she needed to hear it.
But for Sheppard, it meant remembering many painful things about his past, the abandonment by his family, his failed marriage, his fallen friends, all the people he had failed to save on Earth, failing to save someone he had loved, his first love, and most of all McKay getting shot right in front of him. For Ronon, Sateda is a graveyard full of the ghosts of his past. For Sheppard, that is what Earth is. And in order to comfort Teyla in this situation, Sheppard had to dig up a lot of painful memories for himself. He stops for a moment as Teyla thanks her and acknowledges that he had not been able to quite be as open as she had hoped. But he then walks away without saying anything. He may not be able to run forever but regardless of whether he gets caught now and again, Sheppard does not know how to stop running.
Continued in Pt. 11
-* I have opted not to spell her name Melena, which is how many sources have rendered it, due to the unfortunate connotations but it is interesting that the name seems to be composite of Meredith, Lenore and Nancy, all important figures in Sheppard's life -- taking the great big leap here that his mother had been named Lenore. It could be coincidence, of course, but given her use as an obvious narrative mirror and a placeholder for people important to Sheppard, it is at the very least… curious. This also begs the question of what Holland's given name had been. He is frequently called Lyle based on one of novellizations and Charlie likely because his name-tag says C. Holland (possibly for Captain), but we do not actually know his name. Charlie as a unisex name would be fitting given that later on we have a character who is the photo-negative of McKay called Larrin, which is also a unisex name, used of both men and women -- just like Meredith. But of course he could have been something like Melvin, Thorne or Theodor, to go with the scheme... or something else entirely. It remains a mystery.
The team led by Sheppard are making their way toward the jumper bay as per what seems to be his idea for making a get-away, and they do not run into anyone on their way, prompting Sheppard later to say that it had seemed too easy to him at the time. Because basically everything that happens in Sheppard's mental scenario also later happens in the real world, we are able to compare how his idea of how things would go and how they actually go differ. Because there is such a pronounced difference between how things play out in his mind and how they play out in the real world, the replicators may have made a mistake in studying Sheppard's responses to his environment when they should have studied his responses to the people around him, the human element. It is possible that they were simply unable to properly approximate the behaviour of the others in his scenario which was meant to discover how Sheppard behaves in the situation presented to him, the ultimate lesson here possibly being that together they are more than the sum of their parts. In the real world people are messy, rarely rational for more than stretches at a time and their behaviour may be difficult to predict, and yet in spite of this they are able to work together and support each others in ways that the machines cannot comprehend.
As it is, we find them making their way up toward the jumper bay either from the control platform or some other way, the layout of the city mostly identical to Atlantis. Sheppard is at the head of the group being that he is the leader who wants to take care of his people, and he is holding on to one of the guns they had confiscated from the guards. We may note that McKay is immediately behind him, keeping pace with him, just like Sheppard would want him to do. Sheppard has trained McKay to stay behind him when ever they are in danger, and he does not have to tell McKay what to do here, he does it instinctively. This is also something that we see him do in the real world.
The two of them are together at the head of the group and everyone else is trailing after, and we note that Ronon, who is keeping the rear, has given his gun to Teyla. While even in the real world later we see that McKay is staying behind Sheppard and keeping close to him, the difference being that the two of them simply cannot keep quiet when they are around each other, they cannot help engaging regardless of the situation they are in. Sheppard may wish that they were as stealthy as this but they are not. In spite of McKay basically being able to read his thoughts, the two of them cannot help talking to each other, and the tenser the situation, they more they seem to need the attention of the other man. But in his mind, everyone knows their place and what they need to do without a word being uttered between them.
Sheppard: You're the one we like, so don't take this personally.
They reach the jumper bay, and here we see very clearly how Sheppard wishes that everyone knew what they were meant to do without him needing to tell them, without him needing to give anyone orders but that they still did exactly what he wants them to do regardless. Sheppard makes a quip, the dashing hero that he is, and Ronon then knocks Niam out without needing any instruction from Sheppard to know to do it, he just knows that is what Sheppard intended and what he wanted to happen. We see that McKay again had known to stay the furthest back, safely behind Weir and Teyla as they were knocking Niam out. What he tells Niam is that he is the one they had liked, which also tells us that he was a very good choice to function as their host, as the face of the replicators toward the humans. He at least seemed more sympathetic toward their plight, which may suggest that he had heavily featured in Weir's scenario.
Sheppard himself eases Niam to the ground because even though they had been slighted by their hosts, he had no desire to hurt them and especially not the one that had treated them well. Everyone runs into the jumper without needing to be told to do it in an orderly fashion and even though Sheppard is the last one of them into the jumper bay, taking care to see that they are not followed, he is also the first one in the jumper and more than likely he had been the one to choose which jumper to take. His idea had obviously been to commandeer a jumper so that they could bypass having to go to the control platform that presumably would have been manned, as all the jumpers have a dialing device -- which is a clever plan. Sheppard does display his tactical genius in this scenario. One further thing to note is the crumpled condition that Sheppard's jacket is in now that he has been wearing it for what seems like all night. It resembles the way his jacket had looked back when I speculated he used to sleep in his fatigues without bothering to undress at the start of the second season. Likely the condition of his fatigues resembles their state in the real world as the replicators hardly would have had reason or occasion to render them differently.
Weir: What are you doing?
McKay: Preventing the jumper from communicating with the Control Room. Element of surprise.
Sheppard: Nice.
McKay: Go ahead. Dial the gate.
Everyone knows to come in and take their seats except for Weir and McKay, the former staying back to ask what the latter is doing. As for McKay, he seems to know exactly what Sheppard wants without needing to ask as he starts fiddling with the jumper -- in fact knowing to give Sheppard something that he did not even know to want before McKay gives it to him.
We have seen McKay fiddling with the jumpers before in Suspicion (S01E05) and Grace Under Pressure (S02E14), but the one time that Sheppard himself had personally gotten to witness McKay work on the jumper, and he had been working on the exact controls as he is here, had been in 38 Minutes (S01E04). What McKay seems to be doing here specifically is somewhat curious because we have never seen the jumpers communicate with the control room and in fact in The Siege (S02E01), when Ford had used a jumper to escape Atlantis, McKay had told Weir that it had been the jumper that had taken control of the gate and that he had no way to stop him. The fact that Sheppard's mental model of McKay is able to offer him complete control of the jumper and can stop it from communicating with the Control Room is possibly a manifestation of something that he hopes was true, and his belief that McKay can do anything. It also shows us the two of them working seamlessly together, Sheppard behind the controls and McKay paving the way for him. Later on, when they are basically doing the same except that McKay is seated next to him, things do not go quite as smoothly and the tension is making them snap at each other, even though they do work almost as seamlessly together.
Something else to note is what McKay says here, "The element of surprise!" That is something that Sheppard had heard McKay tell him in The Siege (S01E19), only he had not been quite as smooth about it. In fact, McKay had been trying to impress Sheppard and had botched what he had intended to say almost entirely: "In military parlance, surprise… is an element on our side." McKay had clearly felt embarrassed that the cool thing he had intended to say had not landed quite the way he had planned, but Sheppard probably had found his attempt endearing, and it is telling that in his mental scenario McKay is someone who is smooth and knows what they are doing, a real swash-buckling science hero, because there is no one that Sheppard admires more than he does McKay. Sheppard also waits for McKay to give him the go-ahead, seeming to want McKay to give him the order rather than the other way around. Sheppard seems to want McKay to tell him when, and this also happens in the real world -- he waits for McKay to tell him when he can go. And as soon as he does, they are off, and while it is not clear whether the intention of the scenario was to see how Sheppard would react in the situation or it was to gather intelligence, the replicators nonetheless do seem to gain access to the gate address for Atlantis through this scenario, if they did not have it already, and probably the protocols they have in place for gate travel.
Sheppard: Any sign of our new friends?
Zelenka: Still nothing. No unscheduled gate activity, nothing on the long-range sensors.
Weir: I think it's safe to say we made a clean getaway.
Sheppard: Either that, or they're biding their time, waiting for the right moment to attack.
Weir: Well, we'll keep the security teams on alert, just in case...
Next, we find Sheppard back in Atlantis, and from what Weir says, he had been with McKay before he now walks back into the control room to check up on things, finding Weir up there with Zelenka. We did not get to see what Sheppard had done with McKay before sauntering in now, albeit his personal life is something that the replicators likely would have found very easy to extract from his brain given how McKay seems to be the beginning and the end of every one of his thoughts, and how they seem to have used Sheppard in what ever scenario they had created to test McKay's responses with hideous and intimate torture. There is no intimate torture going on in what ever they are digging for in Sheppard, but there may have been something intimate happening that the audience does not get to see. But Weir certainly seems to know that Sheppard had been spending time with McKay before walking in.
Another thing to note is that we see an outside view of the city again from the side in a silhouette the way we had in Irresistible (S03E03), which possibly symbolizes the fact that while we are getting a foray into Sheppard's mind here, we are still looking at it from the outside, from a considerable distance. In contrast to the beginning of the episode, when Sheppard walks up to Zelenka and Weir he does not park himself directly in front of either of them but actually comes to stand in front of the console where we later find McKay, keeping a bit of distance to both of them and actually making sure that Zelenka stays between Weir and himself.
Weir: ...but if they were able to come after us, I think they would have done so already. How is Rodney coming along with the database?
Sheppard: I'll go check up on him.
Weir: I wonder how many other rogue Ancients are still out there.
Sheppard: If they're anything like the Asurans, we're better off leaving them well enough alone.
While both Weir and Sheppard have their radios in their ears that are perfectly capable of checking up on how McKay is coming along with the database -- evinced later by how Weir contacts them both while Sheppard is with McKay in his lab -- they both seem to think that Weir has to ask Sheppard how McKay is doing, and that immediately upon being given an excuse to go see McKay, Sheppard is going to take it.
Weir makes it sound like Sheppard had just been to see McKay and hence asking Sheppard about him would make sense but Sheppard makes it sound like it has been ages since he has seen McKay and so it would be a good time to check up on him. He also volunteers to go down to his lab to see on his progress personally, which is probably not strictly speaking the job of the military commander of Atlantis but the thing of it is, Sheppard wants to go see McKay. What Sheppard does here is basically the same thing he had done in Irresistible and Sateda (S03E04), whether we are to understand the latter as having happened before this episode or after, which tells us that this part of what Sheppard does, Sheppard's response to the scenario, is precisely what he would do in the real world. Going to see a man about a McKay is something that Sheppard would most definitely do in every possible scenario. And in fact we see Sheppard anxious to leave Weir's company for that of McKay here, it is obvious who Sheppard actually wants to spend his time with.
What is less clear is Weir's role in his scenario. We see that she is asking a lot of questions, unlike the others, and we also see her look at Sheppard suspiciously as he walks away, and so it is possible that Weir is actually an avatar to Oberoth in this scenario. Weir may be the vessel with which he is probing Sheppard, which also makes Sheppard's line about him being glad that they had only probed his mind later curious. Here, Weir presents him with the scenario of what Sheppard might do if they ever ran into actual Ancients, and his response is that they are better not seeking contact with them at all. Sheppard is a guardian, not an explorer or a contact-maker like Weir, and as things are in his life right now, he is perfectly content doing what he had criticized the Asurans of having done earlier, which is to "hide from the rest of the galaxy, happy to go on with their lives, just minding their own business." Sheppard does not need more "bad guys," he does not want more complications, he just wants to live life in peace and security. He wants to keep his people safe, not to look out for trouble.
Sheppard: How's it going?
McKay: I've searched a good portion of the database for any indication of the Asurans, but...
Sheppard: Still nothing?
McKay: Still nothing.
Sheppard: Maybe the Ancients didn't want to be reminded of them.
Sheppard walks into McKay's lab through the same door as from we had seen him walk in in Irresistible when he had been fuming about his altercation with Weir, but instead of walking around the table to come stand in front of McKay he now comes to stand next to him. For some reason he goes around McKay so that he is on his right side, where we had seen him sitting earlier in Irresistible when they were discussing Batman, even though he now remains standing. He rests one hand on his hip and the other on the table, his pelvis pointed toward McKay. What is interesting is that the scene begins with a close-up of a computer screen that is running some kind of an experiment, which hints at the fact that Sheppard actually knows what McKay has been doing in his lab besides going through the database as they have him do in this scenario, and that replicators have been able to recreate McKay's lab rather accurately for his scenario. Sheppard knows McKay's lab intimately, and everything that Sheppard knows about McKay's lab was probably of great interest to them.
I have mentioned before that usually when we get moments alone between Sheppard and McKay, which we kind of do here and very briefly at that, there is usually something precluding them from acting the way they normally would when they are alone together and there is no one there to see them. We do not know whether the lab is empty or whether there are, in fact, other people around and we also have to note that while they are probing for Sheppard's responses, the way McKay behaves here is a combination of how Sheppard expects McKay to behave and how he wishes he behaved. What Sheppard wants from McKay is that he treats him as an intellectual equal, as someone that McKay can expect to understand what he says and to grasp his meaning quickly, and most importantly someone who welcomes his presence. Sheppard approaches McKay the way we have seen him do many times before, asking him how "it's going," like their conversation had just been paused while Sheppard had been away from him. And the way McKay responds to him is the way Sheppard wants McKay to respond to him, which is to give him a clear and succinct update while stopping the very important work that he had been doing to give Sheppard his full attention for a moment while Sheppard literally finishes McKay's sentence for him, understanding him perfectly without needing to be told.
The time that they get to spend alone here is very brief. Sheppard could easily have put his hand against McKay's back briefly but does not because McKay is in the middle of typing and he obviously does not know how sensitive what ever he is doing here is, and what is more, they are in the semi-public here. But note the way that just as soon as he finishes typing what ever he had been typing McKay stops everything he was doing and looks up at Sheppard with this open "please kiss me" expression, once again lost in his eyes, that Sheppard just manages to miss, as his mind is already workshopping their problem, trying to find something for McKay to work with, figuring out the answer to the why question -- why is McKay not able to find mentions of them in the database and what the two of them might be able to do about it. The moment is very brief but it is there, McKay looking at Sheppard expectantly and then frowning and turning his face away as he starts thinking about what Sheppard had just said when it is Sheppard's turn to look back at him.
Furthermore, given that this is episode is fundamentally about family, Asurans being scrubbed from the database because the Ancients did not want to be reminded of them resembles what had happened with Sheppard and his own family. Sheppard has scrubbed his family from his database, claiming to anyone who wants to hear that he no longer has any family on Earth. And at the same time, his father and maybe also his brother had scrubbed him from their databases, not wanting to be reminded of him. Sheppard is able to volunteer this motivation for the Asurans because it is something that he has felt himself. But alas, they do not get to workshop this problem for long.
McKay: Yeah, but even if they deleted every reference to Asuras, you'd think there'd be some hint of--
Weir: Colonel?
Sheppard: Go ahead.
Weir: I need you and Rodney in the control room immediately.
In Sheppard's mental scenario he is in McKay's lab engaged in one of his favourite preoccupations, which is trying to figure something out together with McKay. They are puzzling out the mystery of the Asurans, and this seems to be something that Sheppard desires on a very deep level: not being made to feel stupid by McKay but that they are able to figure out something together, both of their wits required to solve the problem.
But he does not get to enjoy this for long because Sheppard's love life is not what Oberoth is digging for, and so they are interrupted by Weir contacting them on the radios that they are both wearing. We may note that she calls him Colonel rather than John here, and even though she calls him John later when it becomes apparent that he is going to have to stay behind to arm the self-destruct, this may be what Sheppard prefers that she call him. Weir calls them both up to the control room because Oberoth wants to know what Sheppard would do in a "Kobayashi Maru" situation, one where he has to face overwhelming odds. But notice again how Sheppard and McKay do not need to exchange words to talk to each other, both of them locking eyes briefly to communicate everything that they need to communicate between them. If there is one thing that has been made clear in Sheppard's scenario it is that he has a deep desire for people to just get him.
We did not get to see the end of the scene with Sheppard and McKay, did not get to hear what words or acts they exchanged before Sheppard left McKay to come to where he is now (although we can be fairly sure that "goodbye" was not one of them). We never even find out why he had come here now that he stands back to watch Lucius seemingly working over Weir and Zelenka, very obviously trying to manipulate both of them into doing something that he wants -- and clearly to great effect. Sheppard and McKay had been alone in a lab with no one else around, and although we did get to see a brief glimpse of how they are with each other when no one else is around, it could be that touches were exchanged and words were spoken before they parted, before Sheppard took off, that were not for the eyes of others. Regardless, Sheppard has come to the control platform from McKay's lab, tapping his fingers on a console as he watches on with what seems to be barely controlled anger. If he had been annoyed by Lucius earlier, it seems to have developed into full-blown irritation. Although he addresses Weir, his focus seems to be entirely on Lucius.
Lucius: Beautiful and brilliant. The two Bs.
Sheppard: Doctor Weir.
Weir: Oh, hi, John. We were just discussing the gate harvesting programme.
Sheppard: Yeah, I heard.
Weir: And Lucius knows of an excellent planet we should investigate.
Tapping the fingers of one hand on a surface as we see Sheppard do here may signal anything from boredom to nerves to impatience, the emotions frequently negatively-coloured. Here, it seems like Sheppard is doing this purposefully as a self-soothing gesture, to keep himself under control because it seems like he is seething, he has had just about enough of this guy. He is tapping on the console to curb his impulse lay his hand on the guy instead.
Sheppard seemed to have walked in in the middle of what ever Lucius is doing to Weir, catching the tail-end of him sweet-talking her. He makes a reference to the "two Bs," which often denote "boobs and butt" (or "beers and burgers," "bed and breakfast") but which Lucius intends to mean "beautiful and brilliant" -- although note how he does not actually call her beautiful and brilliant, he merely implies that he thinks that is what she is and lets her make the inference herself. How the translation algorithm may handle this word-play is anyone's guess. Regardless of his intention, "two Bs" is a crass thing to say but having no game whatsoever does not seem to hinder Lucius from scoring anyone he sets his eyes on.
Although "two Bs" could easily be transferable to men, being that men also have butts and other things beginning with the letter B, there might be a more interesting reference hiding here -- one obviously not intended by Lucius. We may recall that McKay is not given the first name Meredith until McKay and Mrs Miller (S03E08), being one of those obvious retcons, this thing revealed about McKay as though it had always been the case and he had merely been hiding it because he is embarrassed to have a "girl's name," like he tells his sister in The Shrine (S05E04). Curiously, in 1972 a scholar by the name of Michael Meredith had written an article called The Two B's: Browning and Bennett in the Browning Newsletter, discussing the close friendship between the two poets. He quotes from Bennett's letter to Browning:
I have often wanted to thank you, however superfluous the assurance of thanks truly felt might be: and the thanks do not go simply to your goodness in caring to give me your poems, but also to much that is beautiful and good in them: be certain that the "rugged B" sees all the advantage of smoothness when it commends so much that is wise and generous to his fellows as it does in the verse of the other "anything-but-rugged B". But B's of all sorts hive together, and find enough in the various plots of the garden while daylight lasts; and I wish you the fullest of honeybags, very heartily, ever yours
Bennett is obviously playing with words, likening the two of them to bees, and we might similarly liken Sheppard and McKay to bees hiving together, especially currently. But "B" is also close to "bi," and having Lucius reference the "two b's" to Weir while standing between Sheppard and Zelenka might imply something about Zelenka's orientation and why he seems to be so readily accepting of McKay's relationship with Sheppard (and also why later on in First Strike (S03E20) Sheppard's jealousy seems to make him think that there might have been something going on between McKay and Zelenka). Sheppard and Zelenka have also ended up hiving together on Atlantis, broadly speaking. Since Sheppard and McKay were about to start hiving together for real, it could also be that only one of the B's is for "bisexual" and the other is for "buddy," which is what Sheppard seems to call McKay at the end of the episode. The bisexual and his buddy, the two B's, hiving together with their full honeybags. Sheppard at the very least seems to be nesting by the end of the episode. Regardless, it is a mighty strange thing to have this alien to say to Weir.
I have no doubt that many viewers have interpreted this scene as romantic -- as Sheppard being motivated by jealousy, his need to "defend her honour," which is what Weir had teased him with in Misbegotten (S03E02). It is easy to think that he is especially mad at Lucius here because he has romantic feelings for Weir and hence it is upsetting for him to see Weir being pawed by Lucius, to see her acting like a "hopeless romantic," being something that Sheppard had used to describe Weir in The Long Goodbye (S02E16) -- but which had been projection on his part at the time, as it so often is. Sheppard is a hopeless romantic, Weir keeps a tight reign of her emotions to the point of coming across cold and unfeeling a lot of the time -- which of course is not the truth of her, but seems to be the price she has had to pay to come out on top in the vicious, male-dominated world of international politics. But Weir is not a romantic fool, and she is acting unlike herself here, and Sheppard can tell. He has always appreciated it about her that she is not emotionally very expressive, it has made it easy for him to work with her because he knows what to expect. Lucius seems to be disturbing the equilibrium, and he dislikes it.
Sheppard calls Weir "Dr. Weir" here, and while they are usually on a first-name basis -- and indeed Weir calls him John here -- it is not uncommon for Sheppard to call her Dr. Weir in front of strangers, when he wants to remind either her or the others of her position and of their formal, collegial relationship. We had seen both Sheppard call her Dr. Weir and her call him Colonel in Coup D'État (S02E17), either for the benefit of their Genii prisoner or Sheppard's men who were guarding him, being both a sign of respect but also creating distance between them. It seems that here he is using her title because he wants to remind her that she is supposed to be acting professionally and not like a little girl with a crush, like she appears to be doing here, because reminding Lucius of her station is not going to mean anything to him. He does not know what a (non-medical) Doctor even is, and he seems well aware of the fact that Weir is the supreme leader of the city -- being precisely why he is so keen to manipulate her in particular. Sheppard's message here is to Weir, not to Lucius, even though he keeps his eyes fixed on him.
But Sheppard is not jealous of Weir giving her attention to another man because, for one, he may understand by this time that all of the people are acting strangely and therefore not of their own accord. We see later on McKay fall under the spell of Lucius and it is not anger that Sheppard seems to feel then but fear. He knows that McKay is not acting touchy-feely with Lucius because it is something that he feels or has chosen to do, he is not doting on the man out of his own volition, and so jealousy is not the thing that even occurs for Sheppard to feel then, even though he is a very jealous man by nature. He has to watch his lover basically be roofied right in front of his face so feeling jealous of him giving his attention to another is the last thing that he would feel in that moment.
But we do also see what Sheppard is like when he is jealous later on in this very scene, and we can compare his reactions momentarily. This? Is not Sheppard feeling jealousy. This is Sheppard feeling seething rage because a stranger has come to his home and seems to be taking it over, is converting everyone he knows into creepy funhouse versions of themselves. What Sheppard feels here has everything to do with Lucius, not Weir. Him addressing Weir here instead of Lucius is a strategy, it is Sheppard using his skills in psychological manipulation. He responds to Weir in a cool and clipped fashion, purposefully ignoring Lucius even though his entire attention is actually on him. Sheppard keeps his eyes on him as he addresses her, making it clear to him that he is watching him, he has his eyes on the guy and what he is doing.
Sheppard: I heard that, too. We got intel that the wraith recently set up a major outpost there. An alliance of three hives.
Lucius: No. Really?
Weir: Has your intel been verified?
Sheppard: We haven't put boots on the ground, no, but our contacts are trustworthy.
Lucius already knows what Sheppard is telling them and pretends like he does not know, but although he does not seem to be a particularly good liar, it is unclear whether Sheppard can tell that he is lying. He does know that the man is untrustworthy, however, having described him as a snake oil salesman earlier, and so he seems to be trying to figure out what his angle is here. Sheppard is always asking the "Why?" question and it seems like he is trying to puzzle out what this man, who seems to come from a technologically undeveloped society, would have to gain by sending their people to a planet occupied by the wraith to be ambushed there. He cannot figure out his motivation for doing something like that. But then, they have come across natives who worship the wraith so maybe this guy has a deal with them or something. Although Sheppard is forced to reveal some of their intelligence as he is trying to convince Weir of sending people there being a very bad idea, what Sheppard is trying to do here is to get intel out of Lucius. But the guy is unctuous, like McKay had described him, too slippery to get a hold of.
Weir starts questioning Sheppard's strategic evaluation of the situation on the ground in front of everyone because she is driven by the need to please Lucius, and Lucius had just told them that he has a "good feeling" about this planet. Because it seems to please Lucius to send their people on the planet, Weir feels like she has to make it happen, and because Sheppard seems determined to stand in the way, she questions his sitrep. And this is the first time in the scene that Sheppard actually shifts his attention from Lucius to her, when he actually responds to her, pays any attention to her whatsoever. He does not know what is going on here but he tries to reach Weir through what ever spell they are under, knowing her to be a smart and rational person who should be able to see the situation for what it is. He has always been able to count of Weir seeing reason at least eventually, even if sometimes it has taken him a while to convince her to see things his way. Sheppard too is used to getting his way.
Sheppard: I'm not gonna send a team down there -- not when there's still plenty of gates to scout.
Weir: John, you are way behind Rodney's quota.
Sheppard: Forget Rodney's quota! I am not sending a team into harm's way.
Even though Sheppard is very obviously vexed, he is able to keep himself under control, to appear cool and collected, up until the moment that McKay's name is evoked. And Weir seems to do this on purpose because she is driven by a compulsion to please Lucius, and hence is willing to do anything to get Lucius what he wants, she is willing to use any means necessary. And Weir knows that McKay is Sheppard's Achilles' heel. Because she is compelled to get Lucius what he wants, she is not pulling any punches and goes right to his proverbial jugular. Weir knows that Sheppard would do anything for McKay, and so she reminds him that they are doing this for McKay, ultimately. The gates, John. Rodney needs the gates!
We finally see Sheppard show some emotion, and it seems that the mere thought of McKay is enough to make him lose control. We see him curl his hand in the air as though to grab a hold of something to shake it. He also closes his eyes in an attempt not to show the others what he is feeling, as though by closing his eyes and not letting them see his eyes he were able to keep the emotion private and hidden from others. But although Sheppard most definitely sounds enraged here, he is not angry at McKay. McKay talking about the gates non-stop frustrates him, yes, but the thing that is eating him up about that is not McKay's excitement for finding and fetching the gates, it is his belief that McKay is motivated by a need to please Carter, whom Sheppard sees as his romantic rival. They may have talked about things for a really long time but it is obvious that they have not discussed this particular topic at any length because they both seem to have made assumptions that may not correspond with the facts. McKay is keen to get as many gates as he can but it is because he wants to beat Carter. He is feeling insecure because Carter had the brilliant idea of creating a bridge between the galaxies and he needs to show her up by being the one to get the most gates and to get them before her -- which is unlikely to happen since the Milky Way has many, many more gates than the Pegasus.
Sheppard thinks that McKay is obsessed with Carter, and although his belief is not entirely unfounded, he is definitely colouring the whole affair by projecting his jealousy. And McKay, for his part, does not get that Sheppard is jealous and possessive of him. It has never even occurred to him that someone could feel that way about him and hence he does not know to attribute the correct motivation for Sheppard's own behaviour. He thinks that Sheppard is being difficult for no reason and that his reluctance to get on with the programme and get them some gates has to be caused by him either not believing in the concept -- or his reluctance toward returning to Earth. And while he can appreciate feeling like there is nothing for them on Earth, surely Sheppard has to see the benefits of being able to visit Earth occasionally, to get stuff from there.
Because McKay misattributes Sheppard's reluctance, he has been trying to get him to see the benefit of the idea even harder, to convince him of why they need to get this done, which is just grinding Sheppard's gear even worse. This is Sheppard expressing jealousy, not the emotionless way he had said "Dr. Weir" earlier. Sheppard has no hope of controlling his emotions when it comes to McKay, he is completely at their mercy. The mere mention of his name is enough to make him lose the entire thread of what he had been attempting to do here, and Weir seemed to know that. She knows where his soft underbelly is and knew just where to strike even though she probably has no idea why Sheppard seems to get so worked up about McKay's excitement over getting the gates. Weir is no fool, however, and had recently observed the way Sheppard behaved when he was forced to watch McKay interact with Carter, and so it is even possible that she is able to use his jealousy against him here on purpose.
The important thing here is to contrast the controlled way Sheppard is able to approach Weir being pawed by a man right in front of his face and him losing control at the mere hint of McKay wanting to please someone else in a perfectly innocuous way. But later on we are also able to compare this, Sheppard having to watch someone he likes and respects having fallen under the spell of Lucius, with having to watch someone he loves fall under the same spell later. Sheppard is annoyed and frustrated here. He is neither of these things later on when he has to watch McKay taken away from him by Lucius. He is helpless and afraid instead. Sheppard cares about Weir a great deal but it is McKay that he loves. McKay is the one person that he cannot ever afford to lose, the one person he cannot live without.
Lucius: You know what? Colonel Sheppard is right. Don't get me wrong -- with all your advanced weapons, you could easily dispose of a tiny wraith outpost, if there even is an outpost, but ultimately, is it worth the risk, no matter how small that risk may be? I mean, sure, people may label you a coward--
Sheppard: Will you knock it off?
Realizing that he was not going to get anywhere with Sheppard Lucius starts placating him, probably figuring that he will have an easier time convincing Weir when Sheppard is not watching them, and so he tries to get rid of the man by telling him what he thinks he wants to hear here. Lucius really needs to get to the planet, he thinks that his life (or at the very least, his lifestyle) depends on it, and that is worth even groveling in front of someone. But he still comes across as disingenuous, a slippery used car salesman. Sheppard is clearly angry as he watches and listens to Lucius work his particular magic on the others, again tapping on the console to keep his cool.
We do not know where Sheppard had received the intelligence on this planet being a wraith outpost, although the Genii are the likely culprits. But we may note that just as soon as Lucius seems to undermine their allies, casts doubt on the veracity of the intelligence they had received, Sheppard seems to take offence at this on their behalf, looking for a moment like a child pouting. But then Lucius essentially calls Sheppard a coward, and it was not necessarily even his intention to insult Sheppard right in front of him, only to convince Weir of the fact that they need to do this because he is desperate to get to the planet. Because Lucius has not had to actually convince anyone in a long time, he does not seem to have the faculty to be very convincing, coming across obviously smarmy and fake to anyone who is not under the influence of his herb. But it seems that being labeled a coward in front of everyone, out in public where his men can also see this happening, is enough to make Sheppard snap and he tells Lucius to put a lid on it. And we can see from the shocked look on his face that Lucius is not used to anyone talking to him like that, it has been a long time since anyone has responded to him in anger.
Weir: Colonel. I think it's worth investigating.
Sheppard: No. I won't allow it.
Weir: John, are you questioning my authority?
Sheppard: When it comes to the security of this base, you're damn right I am. From now on, no-one goes through that gate without my authorisation.
Although we have seen Sheppard mostly go along with Weir's decisions even when he has not been one hundred percent behind them, or otherwise try to convince her to see things his way when he has actually believed that she was in the wrong, we have also seen the two of them clashing head on on a few occasions before, Suspicion (S01E04) and Hot Zone (S01E12) prime examples of this. When Sheppard truly believes that she is in the wrong he is not afraid to say it, and he can even get very unfriendly about it, having raised his voice at her at least twice before. He raises his voice here too, peppering what he says with an expletive.
It seems like for the most part they are comfortable working together in a way that allows Weir to retain civilian authority of the operation but which also means that Sheppard does not have to take the ultimate responsibility even for the military decisions that actually are his purview. But right now, he can tell that she is compromised and as much as he would like to avoid this, it seems like this time he has to take control. The Oath that he had taken upon joining the service had stated that he will support and defend the Constitution of the United States against all enemies, foreign and domestic; that he will bear true faith and allegiance to the same, and further upon becoming an officer that he will faithfully discharge the duties of the office -- which means that he is duty bound to disobey even direct orders that he sees as being compromised. Sheppard does not want to do this, this is among the last things that he actually wants, but it does not seem like he has a choice. Somehow Lucius has drugged these people with the liquid McKay had discovered in his quarters.
Note that Weir is the one who takes a step toward Sheppard first, and she seems to do this in an attempt at convincing him. But it also comes across as intimidation, her tone of voice also vaguely threatening. Sheppard, however, is not intimidated by any of the three people standing in front of him, and he is not above using his stature to impress his will on others. If he is having to take over the operation then he will perform the role of military commander, and we see that he may be recalling not just COs that he has had in the past but also possibly his own father, channeling his old man for a moment as he towers over Weir. Sheppard actually walks up to her and steps right in her face, and again the will-they-won't-they viewers of network television will probably see something erotic in this, that good old unresolved sexual tension, when that is not what this is. Sheppard hates having to do this for many reasons but he feels like he has no choice. When it comes to the security of this base -- when it comes to protecting the man that he loves -- Sheppard is willing to do this, and so much more. But this is not Sheppard when he is turned on. Having to act like his father or some of his more unpleasant COs does not turn him on. Having a woman try to intimidate him into doing something he does not want to do does not turn him on.
Sheppard actually takes control of the gate for the military, which is not a small thing, since the whole point of the IOA is to keep that from happening. He also does not stay around to argue about it because he does not see the point, the others are clearly under the influence of something and arguing with intoxicated people is a waste of everyone's time. As soon as he has said what he had to say, Sheppard turns around and leaves without another word, and make note of the fact that he has no trouble leaving her basically alone with Lucius even though he had his hands on her when he had walked in. Whether it even occurred to Sheppard what might happen to her if she is left alone with him, it does not concern him now because he has other things to worry about. He is horrified when he finds McKay alone with the man later, and he sure as hell is not comfortable leaving McKay alone with him, even though Lucius does not seem to pursue men for sexual purposes. He just does not think about Weir in those terms, it does not occur to him to be protective of her or to make sure that her honour is defended.
After Sheppard leaves, Weir and Lucius have the following ominous exchange:
Lucius: What a terrible cold he must have.
Weir: This is not like him, Lucius. I apologise.
Lucius: He makes me uncomfortable.
Weir: He's really a good man.
Lucius: I don't see it. If he doesn't come around, you're going to have to do something.
Although she is predisposed to pleasing Lucius, and we see her pawing him as she seeks for physical contact with him, Weir is correct that this is not like Sheppard. Under normal circumstances, he would never have taken control because he is not comfortable having the final authority and hence ultimate responsibility on things. Sheppard tells McKay later in Harmony (S04E14) that people often hate in others something they dislike in themselves and it is more than likely that ordering people around had been something that he very much hated about his father. But it is also interesting that Lucius confesses that Sheppard makes him uncomfortable here. It is possible that Lucius feels unsafe around him because he is used to having control over everyone around him and someone he cannot control is dangerous. Here we also start to see the monster coming out, Lucius hinting that he will have to have them take care of Sheppard permanently unless he recovers from his cold -- he too assuming that it must be the cold that is shielding him from the influence of his potion. Sheppard is in more danger than he realizes.
Sheppard had gotten the heck out of dodge when it started seeming like everyone on Atlantis had lost their whole entire minds, and we do not know where he went or what he did after vanishing from sight. We then join McKay in one of the puddlejumpers in the jumper bay where he is with Beckett and Lucius, seemingly in competition with his best buddy on who gets to show Lucius the ropes. Whether they are in the very same jumper as in which McKay and Sheppard had gone on their private mission of scouting for space gates (and what ever else they may have done while they were out) we do not know, nor do we know why (or by whom) they had chosen this jumper in particular to show to Lucius. Regardless, being inside a jumper has to be reminding McKay of Sheppard. There is no way that McKay could ever see a jumper and not be reminded of Sheppard even if they had not shared their first kiss in or by one following The Defiant One (S01E12).
Lucius: So, what does this do?
McKay: That engages the HUD -- stands for Heads-Up Display.
Lucius: “Heads-Up,” I love that!
Beckett: It gives me whatever information I need when flying the jumper: navigation, weapons...
Lucius: You fly this thing?
McKay: I can fly it, too.
Beckett: Yes, now that you received the ATA therapy, which I invented. I was actually born with the gene...
Lucius is sitting in the pilot's seat, which is more often than not reserved for Sheppard, and in which we had in fact seen him seated at the beginning of the episode. Beckett is standing next to Lucius between the two front seats and McKay is standing behind him, both of them seeming to want to get as close to him as possible. But note that McKay has still chosen to place himself where the chairback is between himself and Lucius, and in fact we had seen Sheppard sit much closer to McKay while they had been puzzling over this problem in the lab together earlier. Also in the vein that we had seen him pummeling Lucius earlier, McKay is keeping his hands in loose fists between them, his body language not as open to Lucius as that of Beckett.
McKay looks excited as he is explaining the functions of the jumper to Lucius, and we know that Sheppard likes it when McKay explains things to him. What is more, he is telling him about the name of the Heads-Up Display, which had more than likely been named by Sheppard, since we saw him tell Ford several times that we was not allowed to name things after trying to name the jumpers gate-ships and the planet itself Atlantica -- never mind that Sheppard's initial reaction to Ford naming things had been over the fact that McKay had liked the name Ford had given the ships, prompting Sheppard to tell him that he was not allowed to name anything, ever. It seems that only Sheppard is allowed to name things that McKay might or might not like. Ford had also given the name to the life-signs detector to Sheppard's apparent chagrin, although it may have been at least partially feigned and just friendly hazing of the young soldier. Regardless, the interest in the names of things is something that Lucius seems to share with Sheppard.
It is obvious that Beckett is trying to impress Lucius, seeming to need his attention, to feel like he is pleasing Lucius with everything that he is capable of. Beckett bigs up his capacity to maneuvre the jumper and boasts with his superior genetic make-up, which is not something that he would normally do. Even if somewhere in his heart of hearts he might be proud of his Ancient heritage, it is not something he would even consciously think ordinarily. But now that he has something to boast with here, in competition for Lucius' attention with McKay, he uses his genetics to his advantage. But although McKay tries to match him, it should be noted that McKay has a naturally competitive streak, and he might easily have felt this way even normally with it having nothing whatsoever to do with Lucius and much more to do with wanting to be more like Sheppard, the man that he admires more than anyone. McKay does not like to come in second place for anything. It may not be the most attractive side of his personality but it is a part of who he is, whereas his need to please Lucius above all else is bringing out an ugly side of Beckett -- and showing a rift forming between the best of friends.
Beckett: ...which makes me much more proficient at operating Ancient technology.
McKay: It does not! He doesn't fly this thing any better than I do.
Beckett: Don't you lie to Lucius--
McKay: You have no--
Lucius: Boys, stop fighting. A gene, you say?
Beckett: It's a genetic fingerprint, if you will, which allows someone such as me to operate any technology on Atlantis. I developed an inoculation...
Beckett continues boasting with his superior genetic make-up, clearly over-selling it since all evidence suggests that while he may have a stronger connection to the technology -- albeit not nearly as strong as Sheppard -- it does not necessarily translate to proficiency in using the technology. And in fact the first time that we saw them, McKay had been trying to guide Beckett in using the technology on the Antarctic base, had been trying to teach him how to tap into his natural ability. Beckett may have the natural gene and he may have developed the entire therapy based on his own genetics but his understanding of how to use the technology is not nearly as intuitive as it is for Sheppard.
Everything that Beckett says here is something that Sheppard could say but never would, it is something that Sheppard may think to himself but would never confess to anyone out loud. Sheppard is proud of his Ancient heritage, he knows that it is what sets him apart -- and had made him eligible for the mission in the first place -- but at the same time, it is the cause of a lot of pain in his life, it is something that he detested about his father and his whole social circle, their emphasis on the superiority of the family tree. On some level Sheppard knows that he is better than everyone else but at the same time he wishes that he was not separated from everyone through things that he has no control over because it has also made him lonely, especially after losing his mother.
Now, while McKay can easily make the argument that Beckett is no better than he is in operating the technology, he could never say it about Sheppard, and he has always both envied and admired the ease with which Sheppard manipulates the technology he comes across. It is entirely possible that what Beckett is saying about himself here is something that McKay thinks about Sheppard. He looks uneasy as he watches Beckett say these things, almost as though hearing him say it makes him feel sad, and we may also note that McKay is actually putting more of his attention on Beckett than on Lucius here, watching him and possibly trying to get a read of his face. It is also possible that he is avoiding looking at Lucius' face because he is able to read him just as easily as he is able to read people usually and because he is compelled to please him, he does not want to be able to read his thoughts. Regardless, McKay is turned away from Lucius for most of the scene, turned toward Beckett instead.
Beckett: ...which allows those who don't naturally possess the gene, such as Doctor McKay, to be able to use some of it as well.
Lucius: Really? A gene, huh? An inoculation, huh? That's great.
McKay: You know what's really interesting? If you look at this down here...
McKay continues making uneasy faces as Beckett short-sells his artificial ability to do what comes naturally to him and Sheppard, and more than making manifest the difference between himself and Beckett here, it is probable that it is the divide between himself and Sheppard that Beckett is reminding him of that upsets McKay. Beckett is furthermore reminding him of Sheppard, whom McKay must be starting to miss even if his conscious mind has no faculty for recognizing that at the moment.
While he may not admit it even to himself, on some level McKay has always felt like Sheppard is far too good for him, that he does not deserve someone like Sheppard. There must be some kind of a mistake that had made Sheppard take stock of him, and he is afraid that one day Sheppard is going to realize his mistake. But even though Sheppard's daddy was rich and his ma' was good-looking, he too thinks that McKay is too good for him because the two of them value different things in people on account of coming from different backgrounds, having been deprived of different things as children. Often people are subconsciously looking for qualities in their partners that fulfill some fundamental need, that fill the empty places within, and Sheppard and McKay seem to fit together exceptionally well -- and be complex enough that finding other people to fit in with them in the same way would be borderline impossible. But because these are things that neither man is quick to admit even to themselves, talking about them with the other has seemed insurmountable even if they had talked about things for a really long time recently.
But even though McKay may not have the authentic gene like Beckett and Sheppard, he does have many qualities he can use in trying to impress the man that both of them are now trying to please, which is why McKay resorts to explaining things instead, trying to share his knowledge with Lucius like he often does with Sheppard, and we can see the excitement shining in his eyes just as soon as he gets to talking about the jumper. And we should note that as he is talking about the jumper and how it works he is also talking about Sheppard, and very likely is telling Lucius things that Sheppard has either shown or taught him about the jumper because no one knows them as well as Sheppard does, even if we have seen McKay fiddling with the jumpers more than once. He might know the wires and crystals better than Sheppard but when it comes to the functionality, of actually steering the thing, of using the interface, which is what they are showing Lucius here, it is Sheppard's domain entirely. And no one has watched Sheppard flying the jumper more than McKay, who had actually been taught how to fly (albeit he never did manage to fly in a straight line) by Sheppard himself. The look in McKay's eyes as he starts talking about the jumper, that is all about Sheppard. McKay is in love but it is not with Lucius.
We should also note here that although Lucius is uneducated and lacks a lot of the information that the Earthlings have, he does not appear to be a stupid man but instead has the kind of shrewdness that is often attributed to foxes. It seems like he comes from a meagre background and never had to apply himself but he still seems to grasp things fairly quickly -- and in this, he actually again both contrasts and resembles Sheppard.
Sheppard: Uh, Doc? Could I speak with you for a sec?
Beckett: Excuse me.
Sheppard: I... think there might be something wrong with me.
Beckett: It's alright, son. Admitting it is the first step.
Next, and we do not know how much time has passed since Beckett and McKay had been inside the jumper with Lucius or since Sheppard had walked away from everyone in the gate room, we find Sheppard lurking by the sick-bay. He does not come into the room but stays behind the doorway, looking in from half behind the wall as though not wanting to be seen, and he is trying to catch Beckett's attention surreptitiously. Beckett seems to have been able to wrench himself away from Lucius to do some work, possibly to prepare the inoculation with the ATA therapy for Lucius and hence is being diligent about his work in his need to please Lucius, and we now find him doing some work with a lab assistant. He seems to be focused on looking at something under an electron microscope, this likely being precisely the kind of help that McKay had told Sheppard he would have needed from Beckett to solve what was going on. For all we know Beckett is working on the herb since Lucius has a need of getting more potion ASAP out of the stash Beckett and the others had brought from the wraith-infested planet.
Regardless, Beckett leaves his assistant as he hears Sheppard call out for him from behind the door and assents to exchanging a private word with him because even though Beckett is driven by the need to please Lucius, it has not made him negatively predisposed against Sheppard. Beckett takes a stand in front of Sheppard having his hands behind his back in the same way we have seen McKay stand when ever he has needed to have a difficult conversation with Sheppard as though bracing himself, and it is possible that Beckett is also doing this to fortify himself in the event that Sheppard would say something bad about the person he is infatuated again.
Sheppard pretends to have come to Beckett in search of his help, as though he wants to learn how to like Lucius better and that there is some condition that is keeping him from achieving the same level of like for him as everyone else has. But the way Sheppard makes the confession, clearly wanting to talk about it in private, also makes this analogous to a teenage boy trying to come to terms with his sexuality -- especially when they have started figuring out that their sexual orientation is non-normative in an environment where normative behaviour is expected and encouraged, like Sheppard's own adolescence seems to have been. It is easy for an adolescent to start thinking that there must be something wrong with them if the topic is too taboo to have open conversations about, if they have questions for which they cannot get answers from trusted adults and people who are meant to guide adolescents into adulthood.
As discussed in connection with Allies (S02E20), it is not just possible but likely that Sheppard might have had questions about his own sexuality that he had literally been too afraid to ask, and if all the information he could get was from encyclopedias and sex manuals like the Reuben book, he might easily have come to the conclusion that there must be something wrong with him. That is what all the books he would have had access to as a teenager would have told him. Being subjected to conversion therapy and psychiatric treatment would have done very little to dissuade him from believing this about himself. But even if he is drawing from personal experience for his performance here, what he is doing here is entirely an act with the sole purpose of getting Beckett somewhere alone with him.
And because Sheppard is trying to get Beckett, another man, to come with him so that they can be alone and Sheppard is using his body-language to accomplish it, is doing it by nudging his head in an invitation for Beckett to follow him, this is also reminiscent of clandestine hook-ups, the way that gay men might have approached others for sex within the confines of the military institution that forbade such things. As discussed, it seems like most of Sheppard's sexual encounters starting from his boarding school days would have gone a lot like this -- quick and dirty, not involving a lot of talking, a mutual understanding and taking care of needs with very little romance, always fearful of getting caught and ever shrouded in secrecy, taking place in more or less unclean environments.
The two of them leaving together as though from a shared understanding of going somewhere private is definitely reminiscent of an under-the-radar hook-up. What is more, this is actually an example of the same kind of wordless communication between them as we have seen between Sheppard and McKay, Sheppard not needing to use words to get Beckett to understand his meaning possibly also facilitated by their Ancient DNA, the empathetic Beckett reading Sheppard's emotions as easily as McKay reads his thoughts. This is also an example of Sheppard easily convincing someone to do something for him, to get them to act in accordance with his will without needing to put a lot of effort into it at all.
Beckett's response to him here, that admitting one has a problem is the first step to recovery, is also something that is frequently associated with recovery from addictions but also something that is associated with conversion therapy. And while it is not Beckett's intention to imply that there is something wrong with Sheppard beyond his inability to admit that Lucius is the greatest guy that had ever lived, they are hamming up this analogy with regards to Sheppard in particular. But even though Sheppard has no intention of hooking up with Beckett here and Beckett does not think that that is the reason why Sheppard wants him to go somewhere alone with him, Beckett does trust Sheppard enough to agree to talk to him as his primary care Physician about what ever he has on his heart somewhere private, and so Sheppard gets Beckett to follow him. He does not need witnesses to what he has in mind to do.
After McKay has turned on most of the ship and made it light up under his touch he also manages to dig up some information about the behemoth whose bridge they are all now standing on. Although Sheppard seems to be upset over Norina following McKay around like a puppy, which we could tell by his sour face and the set of his shoulders, he still responds to McKay in a noticeably soft tone. He first tells him that he did good, appreciating everything that McKay does for them, and although Sheppard is often less than liberal in giving out positive reinforcement and frequently couches it in sarcasm to take the edge off, he seems genuine in his words now.
We may also note that although, as noted, they are all gathered on the bridge, McKay and Sheppard seem again to be having a conversation just between the two of them where the others are merely spectating. It is because it is so easy for them to slip into that world of their own that they do it unintentionally, not meaning to shut people out but as the natural result of the fact that they are the centre of each other's universes, that the other man is always their focus of attention. This keeps happening over and over again because they are not just colleagues and friends, they are each other's entire context. And Sheppard seems reluctant to share McKay's attention with anyone.
McKay: And I have discovered the ship's name. It's the Hippoforalcus.
Sheppard: The what?
McKay: Yeah, well, it appears to have been named after an Ancient general... Hippoforalcus.
Sheppard: Well, we're not calling it that!
We have noted that Sheppard seems to have a real need to be the one naming things. This characteristic of his goes back to the very beginning of the show, and it seemed especially to involve the young Lieutenant that was suddenly his second. Ford was young and eager and excited to be naming new things in a new galaxy, and it seemed to be Sheppard mostly hazing the young soldier by not allowing him to name anything, basically messing with Ford to give him a sense of belonging without actually intending anything by it. It was not so much about him getting to name things as it was getting to tell Ford that he does not get to name things. In Rising (S01E02), they have the following exchange:
Ford: Gateship One ready to go.
Sheppard: Gateship One? A little puddle jumper like this?
Ford: It's a ship; it goes through the gate: Gateship One.
Sheppard: Oh no, no, no, that's all wrong.
Ford: Doctor McKay thought it was cool.
Sheppard: Oh, OK. Well, it's official: you don't get to name anything. Ever.
Although in the divergent timeline it had been McKay that had named the vessels gateships and he certainly seemed to approve of the name also in this timeline, it had been Ford's suggestion and Sheppard overruled it, initially because he thought he had good reason: He is the Air Force officer that has also been a test pilot, there are probably not many people out there that have flown more different types of flightcraft than he has (he had been listing the things he has had the chance to fly to General O'Neill while transporting him to the Antarctic base) where Ford was a marine, and furthermore Sheppard had only just recently and entirely against his own will been promoted to the position of highest military officer in the entire galaxy and he was having to learn how to be the boss of his men on a whole other level. He thought that the Ancient vessels were too small to constitute "ships" and hence went for an alternative designation, and he was well within his remit in doing that. But a few episodes hence he continues teasing Ford about it:
Ford: You know, we still haven't named the planet yet.
Sheppard: I'm sure the Ancients have a name for it.
Ford: How about Atlantica, something like that?
Sheppard: I thought we agreed you weren't going to name anything any more?
It was never that he truly disapproved of the names Ford tried to give things, it was all poking good-natured fun at the eager young soldier. In the second case, Sheppard does not even come up with a name to give the planet but seems satisfied that it already has a name for them to discover. Also later on during The Siege (S01E19), Ford further tries to name a planet as Planet Waterfalls and suggests they should give all the planets names, which is a reasonable suggestion, but he does not get a response from Sheppard this time because Sheppard is not in a mood to be teasing the young soldier, he is so worried for McKay out there all alone and without him that he has no sense of humour left in that moment. But at the same time, it does seem true that Sheppard has a need to be naming things, possibly resulting from his childhood where it had likely been his father naming everything, which we can see in his compulsion in naming the wraith -- which naturally also serves as a means of psychological warfare against them, is an actual interrogation tactic.
Here, it seems like Sheppard actually thinks that Hippoforalcus is a terrible name, it is a mouthful, and because it is a real wholeass Ancient warship they have discovered, he does want to be the one naming it. McKay had noted how Sheppard's eyes had lighted up in Aurora (S02E09) when he heard the words "Ancient warship," and even though the gleam in his eyes seemed more than a little to result from McKay's presence rather than the cool spaceship, he does think it is very cool. The warship is cool and naming it would be cool and he very much wants to be the one to do it.
But at the same time, he may also want to poke good-natured fun at McKay or at least share in the joke with him, both of them thinking that it is a horrible name. Sheppard also uses "we" here -- we're not calling it that, indicating that he would want to name it together with McKay later. There is a scene later on in Spoils of War (S04E12), after they have broken up and Sheppard is no longer extending "boyfriend privileges" to McKay, that he seems reluctant to allow McKay to name something:
McKay: Including our friend.
Sheppard: Stop calling him that. It's weird.
Dex: Then what do we call him?
Sheppard: I don't know. Let's go with... Todd. It's a guy I knew in college. He was very pale.
McKay: Todd's a terrible name!
Sheppard: You got a better one?
McKay: As a matter of fact, I do--
Sheppard: You know what? Forget I asked.
Now, we do not know whether the Ancient general Hippoforalcus was male or female. The name seems male although it has no direct equivalent or meaning in Latin, it does not really mean anything. Vessels in the human world are often given female names and the Ancient warship Aurora, named after the goddess of the dawn or someone named after the goddess of the dawn, seemed to adhere to the same convention. Of course human vessels are also sometimes named after generals who may have been male, like the Earth Vessel USS George Hammond, and Aurora may also have been an Ancient general for all we know.
Later on, they come across yet another Ancient warship whose captain is female so they seem to have been fairly gender-balanced in their war effort. There is a slight chance that the writers were aiming at the Latin word fornax (dec. fornacis, fornacum, fornacibus...) and that the beginning of the name is actually some variation of hypo, to go under, which would give us something like Hypofornacus and put the meaning of the name as something like "under the furnace," which would fit in with the name and the theme of the episode. What ever their intention, I have not seen a convincing explanation for the name and while Ancient seems to have some affinity with Latin, they are not the same. What ever the meaning, both McKay and Sheppard seem to agree that it is a bad one and McKay immediately has some suggestions for Sheppard.
McKay: Oh good, then what about...
Sheppard: And we're not calling it the Enterprise either!
McKay: I wasn't gonna say that! Look, for my second choice, though, I'd go with...
Sheppard: How about we name it later?
McKay: Fine.
Sheppard assumes that McKay was going to suggest to name the ship after the TV show that Sheppard himself had mentioned -- unprompted -- earlier, Star Trek. We know that it is a show McKay has watched or at least is aware of through his comparison of Sheppard with Captain Kirk on two separate occasions (with a third incoming). However, McKay's interpretation of Kirk as a womanizer also suggests that he is not a "Trekkie," that he has a surface-level or mainstream understanding of the character. It also seems not to have been his favourite show growing up, as he appears to have had much more of an affinity toward the 1960s Batman that had already ended when he was born but that would have been shown in reruns when he was growing up, and he may also have been watching Lassie, as learned in Grace Under Pressure (S02E14).
But Sheppard's reference to the show earlier does suggest that it is something that they have watched and that they may well have watched together. He makes it sound like it is shared knowledge between himself and McKay, and while we never got to see how the long range sensors were named (they are already named when Zelenka mentions them in The Brotherhood (S01E16) for the first time), but because we have been shown that Sheppard a) likes to be the one to name things and b) was aware of them having been named after a TV show, he may well have been the one to name them. All things considered, Sheppard seems like much more of a "Trekkie" than McKay, and as discussed before, watching the show as a child may have been one of the reasons that had caused him to want to join the Air Force in the first place. But because Sheppard is able to seemingly correctly anticipate that McKay would want to name the ship after the Enterprise, they may well have been watching the show together now on their second tour of Atlantis.
Many people have noted the connection between this scene and Carter telling O'Neill essentially the same thing in Unnatural Selection:
O'Neill: They didn't go for it.
Carter: They didn't approve the mission?
O'Neill: No, they did that. Once they knew the stakes and the whole "fate of the universe" stuff. Both the President and Hammond realized we had no choice. He sends good luck, God speed, and all those things he says when he thinks we're going to die.
Carter: So what didn't they go for?
O'Neill: The name I suggested.
Carter: For the ship?
O'Neill: Yeah.
Carter: Yeah. Sir, we can't call it the Enterprise.
O'Neill: Why not?
Carter: The code name for the project is Prometheus. What's wrong with that?
O'Neill: It's a Greek tragedy. Who wants that?
Carter: Okay. The X-303 it is then.
In this scene, it is like Sheppard is playing the role of Carter as the wet blanket and McKay the role of O'Neill, which is interesting because as protagonists O'Neill and Sheppard are seen as somewhat similar, both renegade soldier boys that seem to fit ill with the disciplined hierarchy of the military. However, if we played out the scene between McKay and Carter, their dynamic would not be the same as between Sheppard and McKay, and neither would playing it out between Sheppard and O'Neill give us the same result. They have similar dynamics but are not the same. Carter is trying to make O'Neill take things seriously while recognizing why he behaves the way he does, whereas Sheppard is clearly messing with McKay here, and he is again displaying his superior knowledge of what McKay is like. We are shown that Sheppard not only knows McKay but that he knows him so well as to be able to tell what he is thinking, what he was going to say -- and it is obvious that he was also correct in this assessment, McKay basically admits it even when he tries to deny that he had been thinking it in the same breath.
However, let us note that in this, they are paralleling Sheppard and McKay with Carter and O'Neill -- the actual OTP of the franchise. They are likening them to a relationship that, although between a man and a woman, played out in the subtext but which was entirely real the whole time, and has been more or less confirmed by the creators as having been consummated after they were no longer working together with Carter as subordinate to O'Neill, but which was rather clearly although never obviously laid out in the subtext. When Carter takes up the post of commander of Atlantis, it is implied that she is in a "long distance" relationship with O'Neill, that they had been together since at least the 9th season episode Deus Ex Machina when Carter confessed to Agent Barrett that she was "not exactly" single, and their relationship is commonly thought to have begun following Threads toward the end of season 8. That is to say, the intimate relationship of Carter with O'Neill commenced around the same time as that of Sheppard and McKay -- actually slightly later.
They never confirm the relationship outright because, as mentioned many times, the franchise had a working relationship with the USAF and was very much a part of the military-entertainment complex, and hence could not show the characters doing things that would have made the Air Force look bad. Fraternization was against regulations and DADT was very much still in effect, so while it would have been impossible for them to ever bring the subtext into maintext regarding Sheppard and McKay, it was likewise unwise to try to maintext O'Neill's relationship with Carter, even though it was heavily implied. And yet everyone knew, it was intentional, they were constructing the relationship in the subtext, in the background, through off-hand mentions, through Carter knowing O'Neill's password, using the other show in the franchise to make subtle references. Carter and O'Neill's relationship was real even though it was never explicitly spelled out. And here we are asked to parallel these relationships, to liken them to each other. To see McKay's relationship with Sheppard as similar to O'Neill's relationship with Carter.
McKay mentions his "second choice," which means that the Enterprise had been his first choice in spite of him emphatically denying that had been the case. This is to say that McKay denies something while admitting that what he said was untrue in the very next breath, which harks back to Sheppard implying that he had not paid attention to the Taranan leader because he was a guy (which he, strictly speaking, does not even explicitly say). Characters sometimes say things that are not true and we are supposed to notice when they are fibbing as we are presented with contradictory evidence. The question we have to ask here is what McKay's second choice would have been, which we are never told. It is obvious that it would have been something other than what Sheppard then names it as, and it could be that his reasoning was similar to O'Neill in not wanting to name the ship after Greek tragedies.
The name Sheppard gives to the sister ship of the Aurora is the name of her lover, the consort of the goddess, confirming Weir's assessment of Sheppard as a hopeless romantic. But we should also mention Aurora's sibling, her brother (making Aurora his sister, Sheppard explicitly using the term "sister ship" referring to it), as featured on the Canadian superhero team Alpha Flight. I had discussed this in connection with the episode Aurora (02E09), Aurora being the name of a superheroine sharing the name of McKay's sister Jeannie, Jeanne-Marie Beaubier. Jeanne-Marie was the twin sister of Northstar, one of the most prominent gay superheroes and one of the first that had been originally intended to be gay and was outed once the Comics Code finally allowed for him to be outed, but who had been written as gay from the beginning and whose orientation had been implied e.g., through him being half-fairy, explaining his pointy ears. The subtext was there from the get-go.
The writers of the comic had needed permission from higher ups to finally be able to out the character, but even after that his sexual orientation was mostly kept in the subtext while him being a mutant was used as an allegory for his homosexuality. Although Northstar is both gay and Canadian, he outwardly resembles Sheppard, being dark haired, handsome and charming, and in personality because he also loves speed, is in fact a speedster with the ability to fly and to go over 200 mph in the sky, and the fact that his parents had been killed in a car accident when he was a child, which I have speculated had also happened to Sheppard with regards to losing his mother. Northstar is in ways like an amalgamation of McKay and Sheppard, he is what their son might have been like. It is not a stretch at all to suggest that McKay might have wanted to name the ship after him, after his fellow Canadian superhero who has to remind him of Sheppard -- or even that he would have figured it for a name that Sheppard might have liked given his love of comic books, of which McKay certainly knows.
The other alternative is of course that McKay had wanted to name it after some other famous science fiction vessel like the Millennium Falcon or Serenity, or even Moya given how half of the Farscape cast had suddenly transitioned over to the franchise. Alas, we never get to learn what McKay's second suggestion would have been because Sheppard suggests that they think of a name later -- implying that they would think of it together -- while retaining the right to name the ship for himself. But because ships are symbolic or relationships, ship names are interesting. While O'Neill had a whole class of ships named after himself, O'Neill and Carter's relationship never got a proper shipname in the fandom. And it is interesting that people generally recognize their clandestine relationship when we were given so much more in the way of subtext for these two absolute geeks. This scene is a tacit acknowledgement of Sheppard's relationship with McKay being the central relationship of the show. Even the viewers failing to see a hint of the subtext have to admit that.