they thing is, carter's 'scully left mulder bc he got so depressed and mentally ill so she had to leave for His Own Good/For The Implementation Of Gratuitous Mulder Manpain' post canon character decision is that Scully simply wouldn't.
She would not leave him.
Not in a 'she loves him too much to leave him, isn't it romantic' way, though.
She Wouldn't leave him in a 'they're too enmeshed by then to even seriously contemplate it, he's been literally dead before and also on the run apart from her and she never considered them Over, and then they spent a good few years on the run together in the 00s in not even slightly cheery circumstances, and if, after 20 years of unconsciously warping themselves around each other's neuroses and serious trauma, she can lift her head up far enough from their personal morass of dependency and compensation to see that he's depressed it'd be a feat. She might, with this clarity of vision, at times consider leaving to 'shock' him out of it, but she Can't because he's her whole support system and his belief in her and his persistence is the bedrock of her continued functionality in the face of stupendous loss and confusion by like year 3 of knowing each other, and not having him or his vision of her to lean on was bad enough when there was literally no other choice. So. No, even in the midst of that through process, she probably wouldn't really go all the way through with it.
But it's equally likely that, just like in rocky eras of their earlier FBI days, she'd only be able to accurately see how much he was struggling very intermittently, and mainly just start subconsciously altering her behavior and frame of mind to accommodate him or meet him, while maybe having the instinct to try to aim them at some kind of goal or occupation (ie some kind of warning signal going in the back of her mind that says understimulated Mulder is unhappy, though probably not that bluntly coherent).
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