The X-Files Season 11: 10 Things We Learned From My Struggle, Part III
2. Fox Mulder Is Not William's Father
The bombshell to end all X-Files bombshells. The fallout from this particular plot twist is currently worming its way across the internet, striking down hardcore Mulder and Scully shippers left and right. But hold tight - because the news isn't as bad as you think.
Fox Mulder is not the father of William. In fact, William would technically be his half-brother. That's because the Smoking Man (who actually, supposedly gives his real name early in the episode) is the father. CSM reveals this to Skinner when trying to convince the FBI's Assistant Director to join him. The episode then flashes back to season 7's En Ami, where Scully and the Smoking Man take a little road trip, only for Scully to awake alone in a bed in the man's supposed home.
To Skinner, the shadowy figure claims that he impregnated Scully, hinting that it was science that brought about the first super human child. In other words, he crossed his DNA with alien DNA, then artificially inseminated the FBI agent.
As bizarre as it seems, this isn't out of character. The show address experimentation on unsuspecting women early in the series, a plot turn that left many dying of cancer — Scully included, though it was later cured. This twist also does away with the ridiculous "miracle baby" / second coming idea introduced back in season seven. And no, it doesn't stop Mulder and Scully from loving one another, so put those pitchforks down. No doubt Mulder will still be seen as the father figure.