It was implied in the episode "all things" which aired during Season 7. During Season 8 is was also implied that Mulder was the father of Scully's baby. In the recent movie, "I Want to Believe," there was a scene where Mulder and Scully are talking while in bed together.
Scully tells Mulder that is pregnant in "Requiem",before Mulder's abduction she say that to him.
The FBI
Fox Mulder-a believer Dana Scully-a skeptic Walter Skinner-Scully and Mulder's boss and friend at the FBI John Doggett-Scully's partner while Mulder was missing Monica Reyes-Dogget's partner
Fox Mulder and Dana Scully are the lead characters in 'The X-Files' . They are FBI agents.
It was implied in the episode "all things" which aired during Season 7. During Season 8 is was also implied that Mulder was the father of Scully's baby. In the recent movie, "I Want to Believe," there was a scene where Mulder and Scully are talking while in bed together.
"Scully loves Mulder and Mulder loves Scully, it's a wonderful romance" - Chris Carter (creator)
In the episode "All Things" in season seven, it is implied that Mulder and Scully sleep together. The episode begins with Scully getting dressed in Mulder's bathroom, meaning she was also naked in his bathroom. It is known that the only bathroom in Mulder's apartment is off of his bedroom, which means that Scully had to have been in his bedroom with no clothes on or walked through his bedroom with no clothes on in order to be getting dressed when we first see her. This raises the question: why was Scully undressed in the first place? Then, when the camera pans out, we find a sleeping Mulder, lying on his bed covered with a sheet and apparently nothing else under it. This means that Mulder and Scully were both undressed. Did they sleep together? I think that's what we're meant to think. So that's one possibility: Scully was impregnated that night by sleeping with Mulder. The other possibility apparently is that Scully got pregnant by implanting embryos into her uterus. We find this out in the episode Per Manum in season 8. In this same episode, we find out that Mulder provided the sperm for said embryos. Mulder and Scully also hint that he is the father before kissing in the final episode of season 8 and Scully refers to William as our son in The Truth, the series finale. So, the best guess is yeah, he's the father.
scully nicknamed mulder "spooky"
Scully tells Mulder that is pregnant in "Requiem",before Mulder's abduction she say that to him.
The FBI
Scully shot Mulder in self-defense while under the control of a chemical compound, to protect herself from his advancing threat due to his changed behavior. Their connection and trust helped Mulder survive.
*spoiler* After breaking up briefing during IWTB, they make-up at the end of the film. Near the end of the credits there is an Easter egg, showing Mulder and Scully together.
It was implied in the episode "all things" which aired during Season 7. During Season 8 is was also implied that Mulder was the father of Scully's baby. In the recent movie, "I Want to Believe," there was a scene where Mulder and Scully are talking while in bed together.
Fox Mulder-a believer Dana Scully-a skeptic Walter Skinner-Scully and Mulder's boss and friend at the FBI John Doggett-Scully's partner while Mulder was missing Monica Reyes-Dogget's partner
Scully's Theme
They don't really get together until the last episode of season nine,"The Truth". When they run away together as fugitives. But in season seven mulder kisses scully on new years "Milenium" and he kisses her again at the end "Existence" of season eight and nine,"The Truth".And we can see a scene with Scully getting dressed in Mulder's bathroom,in "All the things", she comes apparently naked and we can see Mulder half undressed and apparently totally undressed.