This was incredibly cute, and very thought-provoking, even though this particular dilemma has come up several times in fan fictions I've read.

Something about yours, probably the way in which she denies herself and simultaneously knows that either way, to make love or to run, would be a mistake, is very good. It also seems to scream "NEVER-WILL-GO-THAT-FAR" and yet, in the background, you can hear whispers of "Soon, soon, soon...
I do have some critique, however, that I hope you'll view as just a friendly encouragement. It got kind of hard to read with the constant, huge paragraphs. It would look much more professional, edited and easy if your paragraphs were shorter.

You should keep writing. You're immensely good at it.

oh, it was so sad and so beautiful! you're a really great writer! it captured the mulder and scully relationship perfectly... please write another one!

Great story, very nicely written. The ending was great not opting for the obvious, but also leaves it wide open for a sequel.

AAAAAAH! I love this! PLEASE PLEASE PLEASE write more!