That's why I don't ship Scully/Doggett. At least not by season nine. When he first showed up--after she got over her initial intense dislike of him--I can see him being her Big Strong Guy To Hold Onto while searching for Mulder. And with Luke and everything, I can completely understand protective!Doggett over Scully's pregnancy. So they coulda...maybe.... Once Mulder was back, though, she was utterly unavailable for anyone else. Reyes would certainly be more open to alternative relations than any of the rest of them. Don't see Scully as being into random shagging, though, and she was totally fixated on Mulder by the time Reyes came along. Reyes/Krycek made me laugh at the utter silliness-and-yet-hotness of the concept. Another thing that would only work in an AU.