Maybe that last time was when she decided, half-heartedly it seems, to try to move on and go on a date.

She can't ask him for what she wants because she knows what the answer will be. She's always known. Surely that was one of the things that kept them apart for seven years--Scully's barely acknowledged desire for a life apart from the X-Files. It comes up again and again in the series. To me, Mulder just isn't a stay-at-home kind of guy, certainly not as long as the truth is out there. Maybe not ever.

The sense I get from this story is that they tried to be together -- the hopeful ending of "Existence" fits that. What happened between that time and when this story is set comes out in dribs and drabs.

Yeah, the story is very well-constructed to feed the reader just enough information. And it's all shown. No lengthy exposition required, or endless internal monologues. She makes it look easy but it's not.

I don't see Mulder's outburst changing things between them, however. In the end, though Scully decides to let him stay that night, the larger issue is still there, and likely always will be.

Which is why this story doesn't need a sequel, imho. Let the reader construct a happier ending--if they can.