Herein, who did Scully get pregnant by?
I don't know what you're up to …” In the season 7 finale, Scully learns she's pregnant. The new season premiere concludes with CSM explaining to Walter Skinner (Mitch Pileggi) that he impregnated Scully to create “the first superhuman child.” Skinner demands to know who William's father is if not Mulder.
Furthermore, did Mulder and Scully sleep together in all things? Yes they did. It is implied in the episode "all things" and also confirmed by a villain (the mustached magnetite guy) who says he has been watching scully for a while. The episode "empedocles" reveals that scully tried in vitro, but it failed.
Keeping this in consideration, how did Mulder and Scully have a baby?
A doctor said in vitro may be a viable option for having a child, so Scully went for it with Mulder involved. Basically, CSM claims that during the Season 7 episode “En Ami,” he impregnated Scully “with science” during their road trip.
Who is the father of Scully's baby?
But as viewers learned in the season 11 premiere, William was not biologically Mulder's son — he was CSM's, who drugged and medically impregnated an unwilling Scully. (CSM is also Mulder's biological father.) William kept his Mulder persona, and confronted their father on a dock … who shot Mulder/William in the head.
