Do you think Mulder viewed the office space as "our" office space or as "my" desk and Scully's area over there? How do you think Scully saw it?
There are times when Scully seems more comfortable sitting at his desk than others. At first view, I thought she was comfortable at his desk in "Never Again", but upon further viewing, I interpreted her as maybe hesitant sitting there and Mulder not minding her sitting there and seeing it as an "our" space until he threw his little tantrum of saying that he worked hard for the xfiles while she was just assigned to the xfiles. That is where I saw he, even as much as he tried, was still territorial of his space even with Scully. At the end of the episode, I got a sense that she didn't feel like she belonged in the space and that she probably saw it as his office because she walks in, pauses a minute, looks around, and then moves once he enters his space and "allows" her in. Even the way she sits down is tentative and how she sits in the chair is uncomfortable.
I think there is a point when Mulder welcomes the office to be a communal space because we see the pregnancy book and the couple of pictures of them, but when does that happen? Is it an "us" spabce? Who, in your opinion, would put up their couple pictures in the office? I think it would be Mulder because he is more of the sentimental one and he is already seen as someone who puts up his sister's picture, so he likes to literally see what he values and what matters to him. Interestingly, he doesn't have a picture of his mom on his desk or at home.
I don't recall if the Mulder/Scully pictures are up in season 8 &9, in his home office in IWTB, or in the Revival. Did you see the pictures return, or did they just get rid of them?
TL;DR:
The desk functions as a mouthpiece for the current state of the relationship. Mulder considers it theirs, though he sits behind it; and thinks Scully's insistence on having her own means she is drawing away from him. Scully, meanwhile, reads his lack of forethought as lack of consideration; andm consequently, withdraws.
I'm pretty sure she did have a desk in the early seasons. At some point that went away; and that, too, is interesting-- that perhaps Scully didn't ask for another one because she, too, felt like Mulder's desk was communal... until she began to doubt her place on the files.
Lack of vulnerable communication really affected Scully's perception and Mulder's translation, a crack that split open in Never Again and was resolved (mostly) in Field Trip.
Lastly, I think the office pictures were stored away; but I'm not 100% certain. Samantha Mulder remained, though.
Too Long, Wanna Read:
I think Mulder saw it as an "us" space by the close of Season 1 (if not right after the Pilot.) However: he does have a protective streak, eagerly willing to share territory only IF he and his ideas are taken seriously. Not territorial so much as battered by the world, and sore.
In Never Again, he's stung by Scully's "Refusing an assignment? It makes it sound like you’re my superior" and snaps at her dismissal. Yet, he's immediately shaken by her "And it's become mine," asking in a smaller voice, "You don't want it to be?"
The episode was about Scully's other fathers and endless lines, but it was also-- at its core-- about the lack of communication between both partners. Mulder believed Scully wanted to be there... but did she, really? Did she truly value the work, or was she just there to do her job as a scientist? And likewise, Scully thought that Mulder needed her there but came to wonder if her presence had left any impact on the files.
It's a question they sort of answer by the end of Season 4 and into Season 5-- Scully wants "to work... for my own reasons" in Memento Mori; and she comes back to work-- and Mulder-- as soon as she can (by Detour.) However, Mulder is still holding back; and that breeds, again, a sense of displacement, i.e. The Pine Bluff Variant and The End. By Fight the Future, he's forced to speak the truth; and Scully is stunned over how deeply he valued and needed her.
Then in Season 6 they have no files, and must rely on each other again: Season 2 but with a clearer understanding of their current dynamic. Then they get the files back and flitter about in limbo. And finally, we get a resolution to Never Again, in a way-- Field Trip, where both are in a place where Mulder can just say what he's always thought:
"Scully, in six years, how... how often have I been wrong? No, seriously. I mean, every time I bring you a case we go through this perfunctory dance. You tell me I'm not being scientifically rigorous and that I'm off my nut, and then in the end who turns out to be right like 98.9% of the time? I just think I've... earned the benefit of the doubt here."
He's jaggedly forthright and it hurts her feelings (of course); but it's the same sentiment that she's subtly (and not-so-subtly) maintained all the years they've worked together (in all the Vince Gilligan episodes, particularly): Mulder, there are no such things as vampires; Mulder, there isn't a bug person creating zombie people; Mulder, we didn't see a spaceship in Antarctica; Mulder, you didn't see me on the Queen Anne. Mulder's dark thought in the back of his head is that Scully has felt this way, truly, for years-- since the start:"Tell me you think I'm crazy"/"Mulder, you're crazy." It's a toothless speculation when all is well... but not so much when things are rocky between them.
Scully, in Never Again and Field Trip, feels dismissed and reduced, simultaneously not communicating her own hurt-- or becoming uncomfortable when doing so-- and not realizing that her partner is suffering in the same way. His "passion, dedication, and strength" that she relies on is something Scully is afraid to fully trust, just as she's afraid to fully commit to any one path or afraid to let anyone in too close. Mulder and Scully are both avoidant, scared people who would rather circle the drain than spell out their grievances; and because of this, she would rather "do the work" and hope her message comes across (i.e. hope that he doesn't consider her a spy or a burden or someone who "held you back", as she's sometimes wondered, and feared, from the start) than speak the truth out loud.
As much as Mulder prizes her challenging honesty and her unbending scientific rigor, he also feels dismissed by it-- just as Scully feels overlooked by his zeal for the work or the next "truth."
Field Trip resolved that divide; Biogenesis-Amor Fati widened both their minds (literally and figuratively); and Millennium was just the conclusion of their arc together, with Closure and all things book ending their separate, personal journeys.
So: Mulder always thought of the place as Scully's, that the space in the back was "hers"-- that she had claimed it. This was news to Scully (and not good enough, understandably); and when she challenged it, he offered to get another desk. That never went anywhere, and the topic was never brought up again; but I think there's a part of Scully that just accepted things the way they were. And to Mulder, that meant integration.
Was it resolved completely on-screen? Not really. Was it a part of their relationship that became habit between them? I think so. I also think Scully only returned to the "your and my desk" dividing lines-- or lack thereof-- when she was questioning her place in the world and peace in her choices (Never Again's lasting legacy and "other fathers", all things's identity and peace and "other fathers.")
In short: Mulder considers the desk (and basement) "theirs"; but because he didn't explicitly communicate this for nearly six years, Scully was left to decipher her place there depending on her current confidence or fluctuating sense of displacement.