This was a really interesting episode to revisit - a voyage into Scully's viewpoint, something that has been building up within her all this time. It's perhaps fitting that the questions she asks of herself and her life are the same that many female fans have posed indignantly again and again. Why doesn't Scully have her own office, her own desk? Why does it seem that Scully is always following Mulder's orders? Why doesn't she get to choose the case they're going to follow?
Of course, these answers don't all reflect the choice of the producers or writers of the show to sacrifice character to plot. Instead, it provides an insight into Scully's character - an emerging co-dependency between herself and Mulder that she is trying to fight off, even as late as the 4th season. The re-evaluation of her life is coming because of forced stimuli, but in reality they are all questions she should have been asking all along but probably have suppressed due to other concerns. Although the two stars spend only a few, tension-filled moments together and those moments are painful to watch, it's a necessary phase the agents have to pass through in the growth of their relationship. Before they fully accept the others' permanence in their lives, they must deal with the chafing and perhaps stifling feeling of not living a solo life anymore. For Scully, she needs to justify her inevitable following of Mulder's orders by acting out and also listening to her self-destructive desires and tendencies.
I think the most revealing part of the episode is Mulder's very last line. Scully tells him that not everything is about him, and that this is her life. Hurt by this and his perception that she is acting in rebellion against HIM, Mulder tries to understand her but retorts with a, "Yes, but it's m--" and stops himself. I believe what he's about to say is, "Yes, but it's my life too." It shows that Mulder is ready at this point and is undergoing the process of accepting that Scully is becoming a permanent and necessary fixture in his life. This comes easier to Mulder because, in a way, he's been waiting his whole life for someone like Scully to come along. But Scully resists the idea - that's what this episode is all about - and Mulder seems to recognize her reluctance to really let him into her life, all the way, forever. It hurts him, but he can't do much about it but wait for her to either bail on him or commit.