I'm having so many feelings about Season 1 Jon and Martin right now, and they might be controversial so using this Season 5 conversation as the backbone to this piece:
I'm going bold and I'm going to make the claim that neither Jon OR Martin were in in love with each other in Season 1. Now before you send a pipe bomb to my address, I do think Martin and Jon have always cared for each other. With that out the way:
I know the Martin point is going to be harder to sell than the Jon one, so let's go over that first. Martin has always been connected to The Lonely, which is not just being alone, it's finding comfort in solitude. And his crush on Jon is basically a reassurance that he's going to stay in that comfort zone. From Martin's POV Jon is unattainable: He's his boss, older, and seems to straight up hates him. It looks like there's no chance for connection so Martin feels safe daydreaming, unlike he would if he liked someone like Tim who would be at risk of returning his feelings, and disturbing the loneliness that he had known since being introduced to the concept by his Mother.
Personally, I don't read Martin's crush on Jon as something that's 100% real. I think he cares and frets for Jon, as he cares and frets for most people (in the early seasons especially ) but I think at it's core, his "crush" on Jon is something safe that lets Martin have both the solitude and connection he craves.
Meanwhile, Season 1 Jon is tricky and I'm not going to pretend he's not. For every moment he invites Martin to live in The Institute after being attacked by Jane, he also has a moment where he sends Martin to a murdery puzzle lady with the full awareness that the supernatural is real. Also, if you read the dialogue in the text above, Jon doesn't really explicitly doesn't say that he didn't hate Martin. He puts the words in quotes but doesn't really elaborate on how did feel. Then he tries to make it sound a little better by being like "I just implied I hated you," but he doesn't confirm that he didn't hate Martin. In fact, he doesn't really say anything in this scene that explains his actions.
So with that said, do I think Jon hated Martin in Season 1? No!
He has a lot of moments that show he cares about Martin. Just off the top of my head: He lets Martin stay at The Institute after the worms and buffs the security to keep him safe. He trusts Martin enough to let him describe things for him for the tapes in "Infestation." He also opens up to Martin in this episode about not being a skeptic and feeling scared in The Institute. He even describes what they're having as a "heart to heart." In the next episode, "Human Remains," Jon also comforts Martin when Martin is upset about getting separated because of the worms.
But! You ask, and if you didn't let's pretend you did: "How do you reconcile Jon caring for Martin with everything you said in the paragraph about him being tricky. Well that's because I personally think the simplest answer here is that Jon cared for Martin on a basic human level. However, did not like him that much.
Which I think is the point!
Back to Martin's loneliness, in Season 1 Martin is putting up a bit of a mask. He's gentle, and pleasant, and views Jon as someone to prove something to which the why the whole Prentiss thing happens.
And all of those parts of his personality are true, but we're also missing the parts of the pieces that make up Martin "murder cheerleader" Blackwood in Season 5. Martin can be manipulative enough to draw The Web, he can be petty enough to want to kill Oliver for waking Jon up, and he's prone to centering his own feelings and relationship with Jon over anything else
And saying all of that isn't a callout of Martin. At the end of the day, he's another flawed character in a show FULL of flawed characters. But my main point is, that there's a lot more to Martin then just a quiet, kind, guy who likes to make tea for others and has a totally real resume.
He's flawed, and in Season 1 when he's hiding those the flaws the most, Jon doesn't really care for him. But then time goes on, and Martin starts to show more of himself. From showing his cunning and manipulative side by staying back to distract Elias during The Unknowing, to showing his vulnerabilities in Season 4, to showing off his more flawed side to Jon in Season 5 due to the unfortunate circumstances of that Season, this is when Jon starts to care about Martin in my opinion.
Jon gets feelings for the most real and flawed version of Martin. The version of Martin he only meets because of the trauma they're actively going through. In the screenshot above when Martin says: "It took two years of crisis and trauma to even be compatible," I think that is a billion percent true, but I think it's true because the flawed and messy versions of each other were always going the ones they fell in love with.
Jon needed to be something more than this unattainable crush that Martin could keep safe at a distance. And unfortunately, it's Jon's trauma and grief of Sasha and Tim that ultimately makes him more down to Earth and someone who's wanting the connection that Martin is not fully engaging with. Then Martin needed to be more than the best side of him that Jon saw in Season 1, because that's the side of him that Jon, an also very flawed person, is able to connect with.
I can't believe this is almost 1'000 words and I don't know how to end it. Uh, TLDR: Jon and Martin are together due to trauma, and Jon likely didn't like Martin at first, but it's WAY more nuanced than that.
