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all of this takes place at some undefined point post-canon, but i'd put it somewhere around directly post-canon to maybe three years post-canon, considering that Neil will probably—now that he has no reason to run anymore and has a chance to settle and live life—crash and burn mentally for some time because his brain and body finally have the space and safety-net to do such a thing
and during that roller-coaster, at some point, the gender feelings/confusion will inevitably come up
the fun angst part pre-canon:
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Neil stared at a dress maybe a little too long at some point or said some incredibly trans-coded things when he was still living in Baltimore or already on the run and Mary was being Mary about it or Nathan suspected something and made his feelings known and thus Neil, a master at dissociating and suppressing, blocked most of those feelings and inclinations out
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(if you envision Neil as being part of a system then an incident like that or the culmination of multiple would be when female alters could appear)
cue post-canon:
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Neil starts feeling weird in his body post-canon—as in, like it's not correct, not really his body → he looks too much like his father, his years on the run have made his body more of a utility and not something that is actually his (the very likely chronic pain he's in is also very likely not helping) + all of his scars make him feel like it is more of a battleground than the body of an actual person
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(at least with the facial scars he doesn't look quite as much like Nathan anymore, but the resemblance is still uncanny)
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it also stands to reason that that is a guy with the loosest conception of what being ‘a man’ actually means
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→ i do think he knows what it is ‘supposed’ to mean, considering he had to blend in for the majority of his life and in doing so probably figured out how other men act and talk and took that as his cu
- → since he was on the run, blending in, taking on different personalities, during a time when most other people (teenagers) are trying out new things, rebelling, finding themselves (or an approximation of themselves) his concept of him is already kinda loosey-goosey
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he may also start feeling this weird dissonance in how people perceive him and how he is addressed to how he subconsciously feels he should be seen (i.e. as a woman)—it wasn't as much a problem before because he was always playing a role, meaning he could detach himself pretty easily, which is nigh impossible now by virtue of him trying to be one person in particular
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since Neil is a pretty repressed person and has probably never actively thought about his gender that much if at all, he shoves the weird feelings down and tries not to think about them
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→ like, he has been living in hell for 19 years of his life—ten of them living under his father's thumb, eight being on the run, and one of them being convinced he was gonna die with the additional bonus of getting tortured; that man’s been Through ItTM, there wasn't much brain-space to consider if being a guy is actually right
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maybe he lingers on weird places on his body when looking in the mirror (when he ever actually does so), maybe he says some very trans-coded shit to Andrew without realizing but Andrew figures there is something there that Neil is repressing and thus makes it his mission to figure out what the fuck Neil is hiding this time (even if it's not on purpose)
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also, Kevin's Queen-cover-up with the reasoning of it being the deadliest piece on the board potentially being the first crack in the eggshell
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Neil getting another oh, I could be that moment unintentionally caused by Kevin
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(Kevin being way too unaware of what's happening right in front of him)
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Neil repressing the thoughts for years, Andrew waiting her out
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and then Neil does something similar to Kevin and, when one night he lets himself be drunk because Andrew is supervising, he just goes on a rant about his body and how it bothers her that it looks so much like a guy's and that not only her resemblance to Nathan is fucking her up her but also just her everything else—Neil letting lose and realizing one drunken night that no this body is not It—but because she's drunk and way over her limit she doesn't really remember it (thank God for Andrew and his impeccable memory)
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Neil lets enough slip through that Andrew decides to see if it would lead somewhere interesting
meaning: experimentation time!!!
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Andrew gets him something slightly more feminine than usual (for Eden's)—because why not, might as well give the trans route a shot! (also, Andrew likes dressing Neil in pretty things, sue him)
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Neil is first a little confused but puts it on because he's still Neil and will wear what Andrew gets him
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from then on Andrew tries to see how far he can push it before Neil puts a stop to it or starts to visibly be uncomfortable in a way that isn't just from the fact that Neil has never worn most of the kind of stuff Andrew gets him before
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at some point, Andrew gives Neil a skirt and Neil looks ready to bolt, just standing there, staring at it and clutching it in his hands until Andrew gently pries it from her and gives her some tight-fitting pants instead
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(giving her pants instead meaning throwing them at her from across the room seemingly not caring about how she feels because Neil can only take so many gentle touches until they start to burn on her skin)
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they shelve that incident for a time until Neil just flat out asks Andrew what his mission is, what he is trying to do
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(cue a long and arduous process wherein Neil has a lot of realizations, Andrew has a lot of realizations, and everybody is happy in the end (and no, don't talk to me about the sports or the mafia aspect that would complicate this journey immensely) (actually do because damn would that be interesting!))