Relationship Issues

Mulder and Scully have a relationship. A very close relationship. No two people could spend so much time, in such intense situations, and not develop a relationship. It is a staple of the detective genre that the relationship between partners is almost sacred. In 'The Maltese Falcon’ (1941), Sam Spade, though in love with Brigid O'Shaughnessy, still 'sends her over' because "When a man's partner is killed, he's supposed to do something. It makes no difference what you thought of him. He was your partner, and you're supposed to do something about it…"
In Season Three, the relationship between Mulder and Scully hits a troubled patch. They'd already gone through a forced separation in Season Two, and found they couldn't live without each other. Playing to gender stereotypes, Mulder finds solace in the arms of Kristen Kilar; Scully stays chaste throughout.
Their's is a difficult relationship. They have such differing views on how the world works. Constantly, they find themselves at loggerheads but, usually, they are able to overcome their differences to keep what they have. Both know how precious it is.
In any true human relationship, there will be a dominant partner; the other makes the conscious decision to conform to their partner's view. This doesn't necessarily lead to a position of subservience, or a loss of individuality. There will be sacrifices made by both but, ultimately, in those moments when the relationship is threatened, one will be more able to subjugate their own needs to the other. Scully does this throughout the X Files.
Mulder is driven. He needs the evidence to support his belief system that otherwise will be, and often is, ridiculed by those around him. Scully has no such need. It makes no difference to her whether Mulder is proven right. Her rational scientific view of the world needs no substantiation. The same cannot be said for Mulder; he is in constant need of justification. If Scully were to be proven right too many times his world would collapse in upon itself.
The relationship between Scully and Mulder is the central facet of the X Files. We keep watching because they are so human. But if Scully reached the point where she simply accepted Mulder's explanation we'd have believability issues. The question is often asked, "Scully, after all you've seen…after all you've told me you've seen…why do you refuse to believe?” (cf. ‘Nisei’)
Her answer, in 'Nisei' is, "Because I need more than you. I need proof." In truth, she doesn't. She just needs to exert her difference to Mulder, she needs to hold on to her sense of individuality. By now, she knows that Mulder's belief in the great conspiracy is more than just the delusion of an agent "outside the mainstream” (cf. ‘Pilot’), but, as a human being, she is unwilling, sees no need, to concede her view of the world. They have fought enough battles for her to be confident that she can hold firm on this one point without threatening the fundamentals of their relationship. She is rewarded for her strength of character in 'Fight the Future’ (1998) where Mulder concedes,
But you saved me! As difficult and as frustrating as it's been sometimes, your goddamned strict rationalism and science have saved me a thousand times over! You've kept me honest ... you've made me a whole person. I owe you everything ... Scully, and you owe me nothing.
They try so hard to keep their relationship together, to make it work. Inevitably, however, it will be strained. Season Three is when it is strained to breaking point.
It starts in 'Oubliette' when Scully misreads Mulder's connection with Lucy Householder. There is no hint of jealousy. Scully just pushes her rationality too far, wading into waters she has no right to be swimming in - and soon finds herself out of her depth. Mulder identifies with Lucy because, as she sees it, he is so "sympathetic to Lucy as a victim" like his sister, that he can't see her "as a person who's capable of committing this crime." Scully is a medical doctor who wrote her dissertation in Physics - 'Einstein's Twin Paradox: A New Interpretation’. (cf. ‘Pilot’) She, unlike Mulder, is not a psychologist. Mulder's response, for once, shows his awareness of an accepted branch of the medical sciences, for he is an Oxford educated psychologist, though not a Freudian:
You of all people should realize that sometimes motivations for behaviour can be more complex and mysterious than tracing them back to one single childhood experience.
It may be that Mulder is still nettled by her gross misreading of his situation at the end of 'Nisei' so that, when Scully tells him not to get on the train, his primary concern is with who has told her that it is "too dangerous". There is a sense that he doesn't trust her judgement. Nor does she seem to understand that there is absolutely no way he isn't going to 'catch' that train. She should know better by now!
It certainly doesn't help that, in '731', she completely undermines his entire belief system. While it is equally frightening that some foreign government may have been "experimenting on innocent human beings", it isn't what Mulder wants to hear. But Scully says it anyway: "Whatever is on that train is not alien."
This is breaking point. Mulder and Scully have spent their entire time together arguing the merits of one view over the other and, usually, she will tacitly allow his view dominance. But here she is stating her disagreement, her disbelief. It is a wounding of their relationship.
It's a wound that stays open and raw for a long time.
The rift deepens in 'Revelations’ where the roles are reversed. Scully is a Catholic - who would have thought? - and Mulder is an atheist. Scully gets to ask him,
How is it that you're able to go out on a limb whenever you see a light in the sky, but you're unwilling to accept the possibility of a miracle? Even when it's right in front of you.
There is a battle of wills going on here. Scully knows that she will continue to follow Mulder wherever his wildest theories take him. For her own self respect, though, she needs to establish a bulwark. She needs Mulder to understand there are things she believes and, as in any relationship, she hopes he can have at least the same level of acceptance that she has for him and his outlandish theories. She is the one disappointed:
No, um, there's a man that I work with - a friend - and usually I'm able to discuss these things with him ... but not this.
It is so true of human relationships, even romantic ones, that one of the partners will be unheard by the other. It is one of the saddest moments in the whole nine seasons. All she requires is for him to show her the same respect, if not accepting of the concepts, that she has given him.
And then all Hell breaks lose!
In 'War of the Coprophages', Mulder meets Bambi!
After all she has been through - the willingness to accept the absurd, the loss of a sister, even her own abduction - and he cuts her off - "Not now" - while she, again, is only giving him the rational and, as it happens, the correct, understanding of what is happening in Miller's Grove.
No wonder that, in 'Syzygy', she has clearly had enough. She is pissed! Understandably. And what does he do? He demonstrates a lack of understanding, callousness even, as he ingratiates himself and flirts with the perfect woman, Angela White. Let alone the immediate connotations of 'white', she's an angel to boot. How on earth is Scully to compete? She may be taking things a tad too far when she says she didn't expect Mulder to "ditch" her - a word with a whole shed full of relationship issues - but, bearing in mind all that has been going on building up to this moment, she is justified in her feelings of betrayal.
So far apart have they strayed that, in 'Grotesque', she is willing to believe that Mulder has stepped over the line and needs him to help her "understand why you have a gun on Agent Patterson". She is probably hugely disappointed that she doesn't get to shoot Mulder - again.
Fortunately, it transpires that Mulder hasn't been possessed by Mostow's demon. He has so many of his own it probably couldn't find room. Even for demons there is no room at the inn. (cf. Luke, 2:7)
This confrontation serves to break the tension. The relationship moves on and they learn that, once again, they can believe in one another. The dynamic hasn't changed, however. Scully remains the one who sublimates her true feelings in order to enable her to remain loyal to Mulder.
This is how human relationships work. One will always dominate and one, always seeking those moments to exert their own personality, will sacrifice. Scully is Catholic. She understands sacrifice. Mulder doesn't.

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