Mulder’s guilt complex when it comes to Scully is so fascinating and so tangled.
Because on one hand, it’s understandable. Scully doesn’t care about proving extraterrestrial life, she cares about Mulder, and her job, and the scientific discoveries that inherently come working with Mulder. And she had undeniably suffered for it, in multiple significantly life-threatening ways.
But Scully didn’t originally join him by choice. He didn’t convince her of anything, or try to sell her on investigating X-files. He didn’t manipulate her, she was just assigned there. It was work, it was just a job. But it’s also Mulder’s personal cause, so he feels responsible for everything that happens.
Scully can’t accept his apologies (in the way he wants) because it was be an admittance that something was irreparably damaged, and that would be admitting to a huge weakness. Which means that Mulder can never fully assuage his guilt, so it only builds and builds and builds, which causes him to be Scully’s version of overprotective, which confirms that she can’t admit such huge weaknesses.
So Mulder does that push and pull, warring with what he wants (Scully to stay) vs. what he thinks Scully should/does want (to leave). And Scully hates it because she cares about him, but I think there’s another reason too.
Mulder’s constant blaming of himself ends up denting Sully’s sense of autonomy. A sense of autonomy we see her struggle with much more post-abduction. She is making choices for her life, and her career, and her aspirations. She makes them in a stable state of mind, and she knows what she’s doing- she signed up to be an FBI agent, there are inherent risks. And yes, her love for Mulder (any type of love) plays a role in that, but I imagine she must be annoyed with how he inadvertently acts like he made decisions for her. That she isn’t thinking straight, or isn’t logical enough to weigh pros and cons.
But she also knows him, so she knows that isn’t what he means. Even if it’s what he’s implying.
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