if you think scully was just 'putting up with' mulder, you need to rewatch little green men & the host. like. she loves him. he's her best friend. when he didn't see her in the hallway she was so concerned, she set up a secret meeting with their little signal and she tried so hard to talk him into being himself. she was so relieved when he made a joke, so touched when he said "i learned that from you" but also maybe even more concerned. and in the end when she says "you still have nothing" she's heartbroken. and then !!! he says "i've still got you" she's just as important as "his work" even if they can't say that outright just yet. she's still there on what he cares about, what's important, what he's determined not to lose.
they aren't partners anymore but she makes sure he knows she's there. she will do all the autopsies, she will talk out the cases. they can still have their debates & banter and all is not lost. and he gets the message! he lets her back in. because yes, he needs her but she needs him too. she wasn't going to give up and how could he deny her? they're so pure. they just love each other so much. they care so much about each other and the work and the world.
scully may not believe what he believes, but she knows he's onto something important. and after e.b.e. they are so together on that. they make the people following them run in circles trying to keep up with them, leaving false trails. it's mulder & scully against the world (for the world) and they can only trust each other.
(side note: i truly think scully is a very trusting person. she had a much better childhood & connection to her parents, she learned it was safe to trust. and when she learned those hard lessons, she's the one who doubles down on "trust no one" and even more so when she understands how trusting mulder really is, how it hurts him in the end. so she distrusts for the both of them. she's more skeptical. until he's gone and she has no one to trust, and she trusts skinner, doggett, reyes, the gunmen. but it's still only to an extent. she never tells any of them everything.)
