The X-Files Season 11 Ending Explained

This article contains heavy spoilers for The X-Files Season 11 finale.

The world is safe from an alien pathogen… for now. The four-part “My Struggle” saga has come to a shocking conclusion that has huge implications for The X-Files if the series is to continue beyond season 11. There’s no guarantee Fox renews the series, though series creator Chris Carter told us he’s optimistic there will be more X-Files stories to tell, even if Gillian Anderson is true to her word and has indeed made her last appearance as Dana Scully.

Before we even begin to consider what the series would be like without Scully (and many fans on social media have vocalized they’d tune out if Anderson is absent), we need to talk through what happened in “My Struggle IV” and how it relates to the whole of The X-Files mythology. We’re going to get into heavy spoilers and try to keep it as impartial as possible. If you’re looking for our critical review of “My Struggle IV,” you can find that here. There’s a plethora of questions to be answered, so we called up Chris Carter himself to help us explain what happened in The X-Files season 11 finale.

The Search For William

Though the exact timeline of the season is murky, “My Struggle IV” picks up with an all-out manhunt for Jackson Van De Kamp (once known as William). As we learned in Season 11 episode 5, Jackson was conceived as part of Project Crossroads, a secret government project to create human/alien hybrids. Jackson was the first successful hybrid, a miracle child carried by Scully (who was thought to be infertile) but concocted by the Cigarette Smoking Man. All along it was accepted that Mulder was the father of Jackson/William, but CSM confirmed he impregnated Scully “with science,” which to be very clear is rape, and he claims he’s the true father of Jackson (on the X-Files timeline, this happened in season 7’s “En Ami”).

Since his birth, Jackson has been sought after by government officials and alien cults (season 9’s “Providence”). As a baby, he displayed the ability to move objects with his mind. These superhuman abilities were stymied when a horribly deformed Jeffrey Spender injected the baby with a form of magnetite (which aliens hate!), warning that Jackson was the final thing the aliens needed for colonization. Spender did it as one final act against his father, the Smoking Man.

For the safety of the child, Scully made the decision to give him up for adoption. Taken in by the Van De Kamp’s, Jackson’s abilities eventually returned as he grew older and the government caught wind. As we saw in “My Struggle III,” Jackson is connected to his birth mother, Scully, through visions of the future. That means all of the season 10 finale, “My Struggle II,” was a vision of the future: What would happen if the Smoking Man got his hands on Jackson and begin a final cleanse of the earth’s population through the spartan virus.

Carter gave us one major clue in the text at the end of the opening credits. The words “Salvator Mundi” (savior of the world) flash across the screen, in reference to the controversial lost Leonardo Da Vinci piece that resurfaced and sold at auction for $450 million. The painting shows Jesus in Renaissance dress as the savior of the world and master of the cosmos. Carter explained to Den of Geek the significance of the message and how it shaped the dynamic of the finale:

“For me, there were three parts to that. We have William’s immortality and resurrection at the end of the show, that’s the final image. We have Mulder who could be considered to be someone who just saved the world by stalling the Cigarette Smoking Man’s plans. Then, we have the Cigarette Smoking Man who actually looks at himself as the savior of the world, sort of diabolically, he was going to start the planet anew. Like the devil, he believes that he is right.”

Erika Price, Mr. Y, and The Second Faction of The Syndicate

Jackson wasn’t only valuable to the Smoking Man. A second faction of the Syndicate was after the miracle boy. Back in “My Struggle II,” Mulder met Mr. Y and Erika Price, former members of the Syndicate now working in the private sector. They told Mulder they’re interested in the colonization of space, but Mulder was skeptical about their true intentions. Price plays a prominent role in the cloud-based digital afterlife in episode 2, and it’s clear the company a government contractor catering towards the 1 percent. Finding and studying Jackson could have given the private company some serious power and a potential guarantee that they have the cure if the Smoking Man unleashed the spartan virus.

They were no match for Fox Mulder, who took out Mr. Y, and Jackson, who exploded Erika into little pieces with his mind in the finale.

So what were the origins of this faction of the Syndicate? The initial concept dates back to the 1998 film The X-Files: Fight The Future.

“We had established that there were other people involved in the Syndicate. Originally, I wanted to explore through the character of Strughold, who had appeared in the first X-Files movie, but I was unable to do that for practical reasons.” 

Mr. Y and Erika Price ultimately became competition to the Smoking Man, and lobbied Mulder to help them achieve their shadowy goals. Mulder, though, cannot be bought.

“I wanted to come up with someone whose path with the science and technology had been acquired, and had been burned from the Cigarette Smoking Man. So he now had an opponent, and that was the character of Mr. Y. The character of Erika Price,” Carter said. “Glen Morgan and I had talked about as having even a more nuanced agenda, which played out in episode two. The idea that the X-Files could have been co-opted by a government contractor was a very interesting idea to us.”

Trust No One (To Die On The X-Files)

How does that old quote go? Nobody ever really dies on The X-Files? It’s safe to say Mr. Y and Erika Price won’t be returning, but some beloved figures in The X-Files may or may not be dead after all.

Skinner, in an act of sacrifice, tried to gun down Monica Reyes and the Smoking Man. Reyes, it seemed, took a few bullets. And Skinner ended up sandwiched between two cars. Did both characters meet their maker? 

“As I like to say, no one stopped to take their pulses, so of course there’s a possibility that they both survived,” Carter said.  

In the climax of the episode, Jackson uses his power to disguise himself as Mulder. He says goodbye to Scully, and runs into the Smoking Man. Thinking it’s Mulder, CSM pulls the trigger on his own son, inadvertently killing the key to his evil plan. Jackson, it appears, is immortal from the final shot and Carter’s own explanation. But Mulder finally takes out William B. Davis’ Smoking Man with several gunshot before throwing him into the ocean. CSM has survived a missle, so surely he could take a few bullets from Mulder at point-blank range, right? Carter, as always, was cryptic about CSM’s fate.

“Scully had these images of him when she had her visions, with a face that had been totally reconstructed. Then, as we saw in episode, the season opener this season, and the season finale, he seemed to have been completely healed, although he had minor scarring. That was by design. He has powers to rejuvenate. So, is he dead? That’s a question that remains to be answered,” Carter said.

Scully’s Latest Miracle

The moment that everyone will be talking about is the revelation that Scully is pregnant. A second miracle child. This time, we really, really hope she’ll have the child in peace. No alien onlookers. And it’s safe to assume, for now, that Mulder is the biological father. Here’s Carter’s take on the big final scene: 

“It was a perfect X-Files moment for me, as was the first pregnancy, really, because of with the X-Files, we’ve seen that anything is possible. As it can relate to these two people’s relationship, that is 25 years in the making and I thought was a beautiful opportunity.”

He continued: “It was the consummation of a tremendous amount of restraint, respect, trust, and loyalty. All the things that I think are all of the cardinal virtues together, that would lead to this revelation at the end of that pier.”

How The Episode Came Together

The breadcrumbs of the William/Jackson arc are all over the later seasons of The X-Files. This storyline was a long time coming for Carter.

“I had those four episodes in mind in that I wanted to tell Mulder’s struggle, Scully’s struggle, the Cigarette Smoking Man’s struggle, and William’s struggle. They were the four characters who, for me, were most central to the mythology of the show,” he said. 

“I had this image of Mulder and Scully being united, once again, with a miracle. So, you got that final image, and that William would be immortal, those were all things I had in mind.”

The season as a whole maintained a focus on Mulder and Scully’s relationship like the series never had before.

“Having been doing this now for 25 years, and that the characters are now 25 years older than we began with, is that they now were looking at life through a new lens, and they were looking at, not just their relationship today, but their relationship in the future. They were looking at old age. I think it’s a luxury to be able to have been with characters for so long that you can tell stories that way.”

What’s Next?

If The X-Files season 12 becomes a reality, they’ll have to address the fate of several major characters – Skinner, Reyes, CSM, and Jackson. If Gillian Anderson is done with the franchise, could we see a similar disappearance storyline like we saw in season 8 and 9 after David Duchovny left the show? Would they do that to a pregnant Scully after all this poor woman has been through over the years? Or could Scully retire (in X-Files years the character will be 54, while Gillian Anderson is 49) and take care of her new baby, while Mulder works with a new partner? Is it even The X-Files without Dana Katherine Scully?

These are questions Chris Carter would not answer, given that he’s spent the last year working on season 11, and surely needs a break. So where do you think could The X-Files go from here? Are you satisfied with the ending? Let us know in the comments and thanks for following along with our coverage of The X-Files season 11!