ROB BOWMAN: There’s a sequence after Mulder arrives back in his apartment to confirm Kurtzweil’s existence and friendship with his father where Scully comes in and says, “I’ve quit, I’m leaving. I’m going off to) so and so, I don’t want to stay because I know you’ll talk me out of it. So I gotta leave now, bye.” So she runs out. Mulder persues her down the hallway, has already confessed to her in the room that now is the worst time of all. “We’re really on to something here. I need you. I need you, I need you.”
That’s the theme of the movie, Mulder needs Scully. Never before has he come to that understanding quite so strongly as he does in this story. So, she’s running because she’s afraid that he’s gonna talk her out of it. So the best thing she can do is just hit the elevator button and go, go, go. She never makes it. This was her first mistake. And Mulder also knows that that’s where she’s headed, is out the door. So, he’s gotta tell her why it is that she’s so important to him. And tell her once and for all that in fact, the whole time that they’ve been together, that the two of them have been together, that she has made him better. She has made him feel not like an outcast, not like discarded FBI trash, but actually somebody that’s worthy of her friendship. That, as he says, she’s made him a whole person.
So in a scene filled with such virtue, such, you know, people sharing their most highest thoughts and feelings towards each other, you come to a sort of pinnacle, respect and mutual admiration that it leads into an intimate moment that neither one of them expect. Or were sort of working towards. It just sort of happens. You know, you just keep going and going and arguing and arguing and all of a sudden it’s not an argument, it’s sort of, you know, “we’re for each other, we’re for each other and we come to the opportunity of a kiss for the first time.” But it’s not out of lust, it’s not out of any obvious reasons or typical reasons. It’s out of just absolute overwhelming respect for one another. Out of that respect comes an emotional response, where you transcend, sort of, logic and thinking and it becomes more visceral and human. The only place for him to go in my mind, to express the next thought is to kiss her.