How was Fox Mulder the father of Dana Scully's baby?

Answer 1

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.

Answer 2

Fox Mulder was not the father of Dana Scully's baby in the television series "The X-Files." Scully's child, William, was conceived through an in-vitro fertilization procedure using genetic material from both Scully and an unknown donor.