Thanks... now bear in mind this is my own interpretation, and I'm not actually saying they did sleep together, I think it's more likely they didn't, but it was at least an era when they could have, unlike the era between Irresistible and Never Again. It's semi plausible they could have between One Breath and Irresistible (Red Museum has a lot of UST- and of course the end of One Breath itself is very warm, although more brotherly/sisterly), but Irresistible is when the abduction is finally no longer repressed by Scully- but continues being repressed by Mulder- and this stops all possibility of anything (consensual) sexual between them because Mulder is too afraid to confront the truth and Scully is disgusted with his self absorption and excuses. Darin Morgan arrived soon after Irresistible and deconstructed Mulder as the romantic hero his brother, Jim Wong, and Chris Carter had sometimes implicitly seen Mulder as. Carter and Glen Morgan and Jim Wong themselves then endorsed Darin Morgan's critical reading of the character in their own later, Darin-influenced episodes of season three and four, leading to the post-shipper (not anti-shipper) masterpiece Never Again.

After Never Again, Carter reasserted control, banning future involvement of Morgan and Wong for various reasons (including probably Fox's desire to have the leading characters get along better than they do in Never Again), and tried to tack on a happy ending to the ship and steer things back toward the warmth they'd once had. In order to create that it required Carter punishing Scully for rebelling against Mulder, and humbling her into a victim who would require his aid, and might thereby fall back in love with him. The solution: cancer.

Scully settles for Mulder, which might open a possibility of a relationship (now on his terms), but I really think it is only after she survives illness, in season five, and becomes combative and restless again, which he finally deals with in a slightly more mature way than previously, that they start to develop a romantic relationship again and finally restore their early closeness (less passionate but more comfortable, and probably more sexual).