The X-Files’ Massive Twist Was Set Up 18 Years Ago

The X-Files is no stranger to game-changing twists and sudden shifts to the status quo, but “My Struggle III,” the highly-anticipated eleventh season premiere, might just contain the biggest shocker of them all – one that was first set-up 18 years ago.

Throughout the episode, in which Agent Dana Scully is searching for her son, the long-lost William, the mysterious Cigarette Smoking Man hints towards a special connection between himself and the medical doctor/FBI agent. In the closing moments of the premiere, he reveals his secret to Walter Skinner: Mulder is not William’s father, the Cigarette Smoking Man is.

While pretty much every X-Files fanatic was floored by this revelation (with creator Chris Carter coming out to defend it), “My Struggle III” shows how the seeds of this surprise were sown all the way back in the year 2000, at the height of Season 7, using stock footage from an earlier episode to reveal that the answers were there all along.

As The Smoking Man informs Skinner of his insidious misdeeds, the audience is treated to flashbacks of “En Ami,” which first aired on March 19, 2000. In the episode, CSM embarks on something of a road trip with Scully, whisking her off on a quest to secure an alien cure, not just for cancer, but for all disease. It’s one of Season 7’s finest and most provocative moments, exploring the compassionate side of CSM to which Mulder and Scully are rarely privy.

Of course, he’s always got an angle, and the episode ends with him destroying the disk containing information on the cure, while leaving Scully (and The Lone Gunmen) with a fake. But why Scully? He could have enlisted the aid of Mulder, or Skinner, or any of the countless assets at his disposal to obtain the information.

Suddenly, with the revelation in “My Struggle III,” everything is made crystal clear; whether or not the cure was real, it was only part of CSM’s plan. His true goal, or at least an additional one, was to impregnate Scully, using “alien science to create the first super human child.” Series mastermind Chris Carter said that CSM is a “figurative” father rather than a real one, so he didn’t literally rape her, but he is still an absolute monster – and a total creep.

The Cigarette Smoking Man has delusions of godhood and even mentions rebuilding the world in his own image; his paternity of William is his own twisted take on The Immaculate Conception.

It just wouldn’t be The X-Files if there wasn’t a subtle extra wrinkle for fans to obsess over. In the flashback depicted in “My Struggle III,” there is one distinct difference from events of “En Ami,” and it amounts to a single line of dialogue. In the original episode, when Scully accuses CSM of drugging her, he replies, “I did nothing of the sort.” She then asks how she got from his car to a bedroom, and he says, “I carried you.” However, in the flashback, CSM instead says, “We carried you, my housekeeper and I.”

Everyone knows CSM is a liar and not to be trusted, but could this tiny extra note of dishonesty have deeper implications as the story moves forward? For now, it’s just another unanswered question, one of many in The X-Files, along with William’s present location, the extent of his powers, and whether or not Scully’s vision of the future, as seen in My Struggle II, will come to pass.

Finally, one last question remains: what happened with CSM’s face? In his Season 10 appearances, he wore a prosthetic to cover up his hideously burned visage (courtesy of catching a helicopter rocket with his face in the Season 9 finale, “The Truth”). In Season 11, however, despite ostensibly taking place earlier, his face is apparently completely healed. Was this just a stylistic choice? Or is there more to CSM in Season 11 than meets the eye?