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10X2: Founder’s Mutation

The X-Files 2016: Introduction | 10X1: My Struggle

Billed as the second part of a two-night premiere by Fox, The X-Files return to self-contained cases with this episode — however in the tradition of many season 1 episodes not all is as it seems and the mythology points its nose midway through.


Spoilers after the jump.

Founder’s Mutation” is written and directed by James Wong, and executive produced by Chris Carter and Glen Morgan.

Morgan and Wong (“the Wongs”) are of course responsible for some of the series’ best episodes, and to a great extent they are responsible for the identity of the show, being the writers of the show’s first non-alien, monster-focused episode (1X02: Squeeze and its sequel 1X20: Tooms); they developed the characters immensely, particularly Scully (1X12: Beyond the Sea, 4X13: Never Again); they created the characters of Skinner, the Lone Gunmen, Scully’s mother and father and sister Melissa; they injected a great sense of paranoia in the mythology (1X16: E.B.E.) and gave the show episodes where the supernatural could be something optimistic and not necessarily scary (2X08: One Breath) as well as some of its most horrific B-movie-guilty pleasures (2X14: Die Hand die Verletzt, 4X03: Home). After they left The X-Files and Millennium in 1998 and after some other projects, Morgan and Wong stopped being a creative duo and went on their own ways; this is the first project in which they work together since 2010. Needless to say that expectations for this episode were high.

The X-Files team in the 21st century

While “My Struggle” checked many boxes of what a classic mytharc episode included, “Founder’s Mutation” does the same for the stand-alone or monster-of-the-week episode: the investigation, the flashlights, an autopsy, questioning people, a debriefing with Skinner debrief, Mulder misbehaving stealing evidence. It really feels like old times! Time has passed and the episode is aware of it, there are jokes on exactly that (“I’m old school, pre-Google“) and the obligatory references to current events closer to the present (Snowden, Obamacare). A lot of subcontracting going on here: the Department of Defense subcontracts Nugenics, Nugenics subcontracts to A-1 Janitorial. Along with quips by Skinner on a monstrous bureaucracy, this is the 21st century all right!

Furthermore, what is immediately striking by looking at this episode is the range of characters we see. There is much more diversity: Sanjay and Gupta are from India, the nurse who helped Scully in “My Struggle” looked Indian as well, Sanjay was gay (was that a Deep Throat joke with Mulder’s informant Gupta?). This is more representative of modern USA; the original show was altogether populated by overwhelmingly white and straight characters. The fact that the show is okay with portraying non-white, non-cisgender characters is an evolution in and of itself! Also, the treatment of Scully and her Christianity is very different from the heavy-handed approach of Chris Carter. Scully uses her connections in the Our Lady of Sorrows hospital to solve the case, and that scene has definitive quips at the audience that the agents are making fun of how Christian conservative this place is. After working in that place for years, doesn’t that bother Scully? All these diverse elements can be attributed to James Wong.


While the series in order to function still has to keep a certain believer/skeptic dynamic, this is not a reboot, the past 23 years have changed these characters. Scully is the one who first mentions alien DNA (!), she is no less a “believer” in this particular case than Mulder. Skinner is not the boss with ambiguous allegiances, he is fully on their side privately and he is willing if not to breach protocol at least to stall bureaucracy and turn a blind eye on the agents’ more extreme actions.

What is jarring in this revival, rather, is how quickly does the show return to the status quo ante, to the way things used to be before 7X22: Requiem put an end to the Mulder-Scully period of the show. A decade and a half after season 7, they are still Special Agents, working from the basement, answering to the same Assistant Director (who has seen no evolution in his career either), doing their shtick. This part of the journey is definitely forced from a desire to return to how things used to be, to recreate the basic canvas of “two investigators into the paranormal”. Given the possibilities that could have been — which we explored at EatTheCorn here — this decision tries very hard to pretend that no time has passed since the nineties.

The previous episode had so much ground to cover that it did not have time to present a full scene where Mulder has to wear a suit for work and Mulder and Scully are reintegrated in the FBI. Granted, The X-Files never lingered much on such expository background “details” but the transition is quick. Could this be because the episodes’ airing order were changed after they were shot? Episode 5 became 2, 2 became 4 and 4 became 5. Carter explained:

There’s a character relationship, emotional arc that spans all those episodes. Even though we’re airing them somewhat out of order. The one that airs as episode two was actually supposed to be episode five but we moved it because we felt it served what was going to be episode two better to reorganize the episodes. But there is an arc that deals with the show’s mythology, the characters personal relationships, the son they have together, William and the emotional story that is familiar to anyone who is a fan of the show.

Was Skinner’s line “Welcome back, you two” added after this decision was made? Were changes made to what is now episode 4, “Home Again“, to make it fit better? We will have to see the rest have a more complete picture.

And it’s back at the FBI, in the same basement office. The door reads the same as old: “Fox Mulder, Special Agent”. No mention of Agent Scully. This coming from James Wong and executive producer Glen Morgan, the writers of 4X13: Never Again, which very memorably made the absence of a desk for Scully an illustration of how out of place Scully was feeling in her life. Frankly, not to give her a desk or a name plate is as unacceptable as Fox still offering Anderson half of Duchovny’s pay after all these years!

The X-File case

The episode itself is a good, solid scary story, with several gory body horror scenes and some memorable visuals, like a classic stand-alone episode. The birds gathering and the teaser in particular is everything an X-Files teaser should be, and the sound editing, camera work and visuals are among the best the series has made. James Wong does a great job directing.

The case deals with young homeless women being used by the military in genetic experiments as incubators, genetically manipulating their babies, then taking them from them, and occasionally killing them if they become a risk of revealing this project to others. A horrible and sordid premise! There is some “X-Men” in this story, or some “Tower Prep”, the 2010 series in which Glen Morgan and James Wong last collaborated, which focused on a mysterious school that groups together children with emerging superhuman abilities, and which was cancelled after one season.

The human story of the X-File is that of Kyle, a victim of his father, ‘the Founder’s mutated offspring’, who wants to reunite with his sister. He is the mutated offspring of Augustus Goldman, the Founder, who is the classic crazy scientist with no trace of feelings that doesn’t hesitate to experiment on his family — or the classic representative of patriarchy, dominating women. Kyle solicits the help of Mulder, perhaps because he was feeling a common history with Mulder’s quest to find his sister Samantha. It is not established how Kyle managed to find his mother in the psychiatric hospital in the first place. Perhaps they share a psychic connection? From his mother he found out about Nugenics, stalked Dr. Sanjay and progressively forced him from a distance to try and steal the data, until Sanjay couldn’t take the penetrating noise any more and committed suicide. Sanjay’s love for “his kids” and the love he and Gupta seem to share comes in sharp contrast with the Founder’s clinical distance with his own kids — another quip at how non-normative love can be superior to a traditional but failed father-son love.

The company that runs the experiments is called Nugenics, a portmanteau of “new” and “eugenics”. The Department of Defense is very secretive about this work, and the episode ends with an armed team of military isolating the building — paranoia everywhere, very fitting coming right after the conspiratorial deliriums of “My Struggle” (the DoD is everywhere yet Mulder, a fugitive, and Scully, who aided and abated, are reinstated in the FBI and the X-Files with no problem?).


The science:

  • Goldman mentions “Proteus syndrome [what most likely “Elephant Man” Joseph Merrick had, and the Great Mutato in 5X06: Post-Modern Prometheus looked like it as well], Crouzon syndrome [cranial deformity; what the boy Scully talks to had], all kinds of cancerous tumors, epidermal displasia [more common among dogs, unless it’s ectodermal dysplasia; Owen Jarvis, or rather Micahel Berryman, the actor portraying him, in 3X11: Revelations has this], Pitt-Hopkins syndrome [cranial deformity, mental disability], ichthyosis [what the father that dies in the teaser of 2X20: Humbug had], Marfan syndrome [long arms], among others“, all existing diseases.
  • The titular “founder’s mutation” is a genetic term for the founding individual of a mutation that is passed on to the offspring; effectively, evolution at work. Mulder: “Every new species begins with a founder’s mutation“.
  • Scully mentions a very specific paper in the episode: “There was a study published last year in Nature Communications, by Batini and Hallast, that found that Y chromosomes in the majority of European men could be traced back to just three individuals from the Bronze Age.” This paper can be found online here! Published in May 2015, the episode was shot some two months later, that is some very good research by Wong! (It was Wong’s, not science advisor Anne Simon’s, as she confirmed on Twitter.)
  • Also, the 2014 Riley vs California Supreme Court ruling about a warrant to search a mobile phone Scully can be found here (thanks X-philes for that one!).

Evolution becomes a theme of the episode, further reinforced by the showings of “Escape from the Planet of the Apes” (Don Taylor, 1971), the second sequel to the “Planet of the Apes“, which deals with experiments on apes in order to make them smarter and force evolution (and of two (ape) parents that are forced by circumstances to give away their son for safekeeping!), and of “2001: A Space Odyssey” (Stanley Kubrick, 1968), which depicted the evolutionary jump from smart ape to humans to something else. Also, one of the children is called “Adam”, as if he were the first of his species — similar to how the first clones of the experiments in 1X10: Eve were all called Eves.



If there is one issue I would have with the episode (apart from Scully’s office!) would be that the end comes too abruptly. Kyle and Molly reunite; Skinner and Scully and Mulder are denied passage by the DoD; and we hear no more of Kyle’s story. Of course a great number of episodes were like this. However, a short scene with Kyle and Molly out in the wild trying to survive, for example, would have provided some emotional closure, and I would have gladly traded some scenes earlier in the episode for more time with Kyle. Naturally, the episode prefers to end on an even more emotional scene, one involving William.

Mytharc links

From the very beginning, Mulder seems to know there’s something larger going on than a weird suicide. He was probably drawn to the case by the connection with the DoD — in fact, maybe Skinner put Mulder and Scully on the case. “This could be another phase of the project– their experiments in eugenics.”

“Eugenics” immediately recalls 1X10: Eve. But the episode as a whole is much more reminiscent of 5X05: Christmas Carol / 5X07: Emily — also because these are episodes that focus on character and start as a stand-alone and develop into mytharc. In Emily, where Scully and Mulder discovered a clinic where women were used as surrogate mothers to incubate in vitro babies that were alien/human hybrids, using the ova collected from abductees. Emily, Scully’s genetic daughter, was a result of that experiment, and Scully had to suffer to see her condition grow worse when she took her away from the doctors experimenting on her, until she died. Apart from William, this case could have reminded her of Emily as well.

Other experiments this episodes recalls are those conducted on teenagers (2X10: Red Museum), who received injections with alien genetic material; by Zeus Genetics (8X08: Per Manum, 8X20: Essence), who used ex-abductees to impregnate them with alien or alien/human hybrid fetuses and harvesting upon their birth; and the chloramine babies program (9X01/02: Nothing Important Happened Today), which sought to modify embryos using biochemical agents carried inside common tap water.



The “powers” of the children in Nugenics recall others that we have seen in alien/human hybrids. The ability to breathe underwater exhibited by young Molly is also another trait shared by (certain?) alien/human hybrids, most notably Dr. Secare in 1X23: The Erlenmeyer Flask. The telekinesis exhibited by older Molly is something we saw William do (if he was a hybrid! 9X01/02). We didn’t see Kyle’s mind control, but mind reading (Jeremiah Smith, 3X24: Talitha Cumi; Gibson Praise, a human with alien genes activated, 5X20: The End). Kyle’s mind connection that expresses itself like a stringent sound is like what Mulder experienced when he started being a mind reader, when the alien DNA he was carrying started expressing itself (6X22: Biogenesis / 7X03: The Sixth Extinction).

Augustus “Founder” Goldman seems to be one more doctor attempting to experiment and study with fetuses and babies and observe their effects. He could be trying to understand whether the syndromes caused by naturally occurring genetic anomalies could be used to better the species and develop specific abilities, to create mutated babies that express specific selected or inserted traits. He might indeed be using alien DNA provided by the DoD (we don’t really know, he didn’t answer Scully’s question) — or he might be trying to activate dormant genes in human DNA that we know are of alien origin (6X01: The Beginning, also mentioned in “My Struggle“).

We had understood previously that such experiments were conducted in order to create the perfect alien/human hybrid in preparation for colonization (6X12: One Son). Now with “My Struggle“‘s upheaval, it is less clear. The titular “founder’s mutation” does point to the creation of a new race: is that a slave race of hybrids to serve aliens, or is it a mutated race of humans resistant to the alien invasion?

What is even more surprising is Mulder’s line: “In 1973, the Syndicate was convened to assist in a project to colonize the world by creating alien/human hybrids. The project was ultimately unsuccessful. I doubt they ever stopped trying.” While “My Struggle” did not put into question the experiments on alien/human hybridization, the colonization storyline was the one that was explicitly discarded. Mulder might still have his doubts (or the episodes feel disjointed).

At the end of the episode, Mulder reveals he has kept Kyle’s blood vial — similar to him having kept Scully’s ova at the end of 4X15: Memento Mori. Perhaps Scully will also test it for alien DNA.


The emotional core of the episode is of course Scully and Mulder’s feelings about William, awakened by Kyle’s story and the Nugenics experiments. The X-Files very rarely spent time exploring the feelings of Mulder and Scully outside of their work, the episodes were usually strictly confined to the case at hand and even in the mythology episodes reminiscence was very rare (2X08: One Breath, 5X05: Christmas Carol). It is enormously gratifying that these two characters are finally allowed some screen time to address something obvious but too little referenced, that they are still in pain after all these years.


William was given up for adoption at the end of 9X17: William because Scully preferred making William anonymous after going through the adoption procedure instead of risking having him close to her, where the aliens and Supersoldiers would know where to find him. This was an obvious way for Carter to dig himself out of the impasse of the season 9 mythology so as to approach a feature film franchise in which Mulder and Scully are free to investigate without carrying around a child. This painful decision tore the fandom apart and shed a very long shadow on the now tainted legacy of The X-Files, all the way to today. Here, Scully (i.e. the writers) justifies herself once more:

Scully: “Do you ever think about William?”
Mulder: “Yes, of course I do, but I’ve… I feel like I’ve had to put that behind me.”
Scully: “He’d be 15 years old now. And I’ve missed every single year of his life. And sometimes… I hate myself that I didn’t have the courage to stand by him.”
Mulder: “You did what you did to keep him safe. His adoption is secret, his location is unknown because you had to protect him.”

As Scully says, “a mother never forgets“. But for some reason, after all these years, Mulder lies about this to Scully; as we see, he is very much still thinking about William. At least both parents acknowledge that William is their son, putting behind the frustrating ambiguity that seasons 8 and 9 had managed to entertain on who the father was. But at the same time, Scully is still worried that he might have been part of an experiment regardless; indeed, some of the experiments we have seen have involved manipulation of the embryo or the young child so even if both biological parents are accounted for there is still the possibility.

The William storyline was so controversial among The X-Files‘ fans and detractors that the writers could have chosen to plainly ignore it and go on — given how other things have been forgotten, like Supersoldiers or Mulder’s status as a fugitive, why not? The fact that he is the focus here is another proof that Carter still wants to use him somehow in the future developments of the mythology. Carter had also told IDW comics writer Joe Harris not to make William appear in the comics as he had plans for him. Possibly in the potential third X-Files film. The episode could imply that, if indeed William develops some superhuman traits due to his possible alien genetic heritage, like Kyle, he will come to seek out his parents in the future.

The episode’s showpieces are two poignant daydreams of “what could have been?” if they had kept William, how their life would have been, living in that same house in rural Virginia as a family. Pleasant fantasies turn into nightmares as they envision their fears becoming true, thus justifying the adoption decision. Whether they manage to justify the adoption decision is up to the viewer — my main issue has always been that, in-universe, given how thoroughly the NSA and the Supersoldiers were using surveillance to track Scully (see 9X08: Trust No 1) it was difficult to imagine how William could become completely anonymous.

The daydreams are triggered by looking at a photo of baby William; this is reminiscent of him looking at a picture of Samantha and crying (1X03: Conduit, 5X03: Redux II). William is portrayed by three different child actors, brothers and sisters of different ages, the Longworth siblings:



In her daydreams, Scully sees herself as the caring mother, worried about her child’s health. This is natural given all the experiments Scully went through, and all the seasons 8 and 9 worries that William might have been the result of genetic tampering. With William’s broken arm, Scully could be worrying that, entering a hospital, William will be identified and experimented on as well.

In his daydreams, Mulder sees himself, naturally, as the “cool dad”! Mulder gets to share with him his passion for space exploration (he quotes JFK’s famous 1961 speech that accelerated the space program and reached the goal of a manned moon landing in 1969, before the decade’s end) and his passion for alien life and the sublime (watching “2001: A Space Odyssey“, an ancestor of The X-Files in the way that it unchained passions in interpreting meaning)! His worries is that William might be abducted, like his sister Samantha was when she was about that age. The scene is of course reminiscent of Samantha’s abduction scene from 2X01: Little Green Men (written by Morgan & Wong).


Seeing these two souls having these thoughts, crying over a picture of a baby, both alone in their respective homes, is incredibly sad, and makes the Mulder-Scully separation even more painful.

All in all, a solid episode tailored to please long-time fans with some good scares, not groundbreaking either, elevated by the choice to dedicate scenes to Scully and Mulder’s inner feelings.


Some final notes:

  • In Skinner’s office there’s a picture of the Arlington cemetary: a tribute to the Lone Gunmen?
  • Kyle’s adopted name is Gilligan: an in-joke for Vince Gilligan?
  • Both Anderson and Duchovny have noticeably hoase voices in many scenes: too much shouting in shooting “Babylon“? too much partying in their trailers?
  • Scully says “All my training, everything that I know about psychology tells me that she’s delusional“, which is odd since Mulder is the psychologist in the couple.
  • You might recognize Sister Mary (Christine Willes) as FBI psychiatric counselor Karen Kosseff, who counseled Scully in 2X13: Irresistible and 4X22: Elegy and also appeared in 2X21: The Calusari!
  • Continuing on from the notes for “My Struggle“, several problems with the Our Lady of Sorrows location. Here, Scully mentions she had worked there for 7 years — so 2008, at the earliest. I Want To Believe happened in the winter 2007/2008, but there it looked like she had been working in Our Lady of Sorrows for years. The hospital in IWTB looked like it was not in Washington DC; perhaps after the events of IWTB Scully moved to another hospital with the same name in DC?
  • Same observation as with the premiere: the use of quickly edited flashbacks to depict the backstory of the characters, here Kyle’s mother recollections, is very modern and gives the feeling of a faster pace. It is different compared to how the old show used to let a scene flow in its entirety, letting the performances of the actors come out more. I feel as some of the subtlety that made the show a success is getting lost; or I might getting old.
  • I didn’t expect to say this, but Mark Snow music at times feels very different from what it used to be. In conjunction with the faster general pace of the episode and the lack of scenes without dialogue, the music has a lot of fast electronic drum rythms and doesn’t have much of that mellow mood-setting atmospheric sound. As if The X-Files is now copying the very shows, like CSI, that itself inspired. We do get some season 4-like oboe instrumentation in the calmer scenes with William.
  • This is the revival’s most expensive episode, because of several scenes shot in exteriors — which is surprising given all the special effects in “My Struggle“!



8 Responses to “10X2: Founder’s Mutation”

  1. Jason says:

    I do hope the blood vial comes up again.
    Mulder’s comments about the syndicate are reassuring that the series is not abandoning 9 years of mythology, only reframing it. The show is dealing with the unprecedented problem of reviving mysteries that were meant to be resolved in “the original series” (your words!)
    For all its flaws, it helps that IWTB can serve as a bridge between The Truth and My Struggle. I think Carter feels less pressed to address the fallout of The Truth since Mulder and Scully have already had one stint back at the FBI in IWTB. Now the context of that stint is a whole other issue and I think that’s the point. Carter wants us to direct those criticisms at IWTB and not My Struggle.
    I really liked Founders Mutation. And thanks for your great work on this site.

    • orodromeus says:

      Thank you!

      Indeed, this was an issue for IWTB.
      Scully’s ova was not brought up until 4 years after Memento Mori, there’s no rush to bring back Kyle and the blood vial!

  2. Sullivan says:

    Great review as usual. We really feel mostly the same about the episode.

    Yeah, to me, and I understand this can feel casual, the fugitive aspect has been completely dealt with in IWTB, where Mulder was given a ‘full pardon’. It only works if the alien invasion has been seriously harmed and the Replicant threat eliminated, but I think Founder’s Mutation is starting to explain us how exactly that happenned (seee my own review).

  3. Tim says:

    Thanks, but it’s in French!

  4. SamSimon says:

    Another interesting article, thanks! You managed to shed light on a lot of positive aspects that I completely missed by simply watching the episode (twice).

    As for your article on the first episode of this new season, though, I don’t fully share the overall feeling of satisfaction about the episode. Although it seems that a lot of work went into making it, I had to watch it a second time in order to fully understand what was going on, and this is not a plus. This time not only the single story within the episode feels rushed (the ending in particular!!!), but also, as you mentioned, the “back to business as usual” for Mulder and Scully is hard to swallow. I think that this episode could have worked better with more time devoted to the mystery (and possibly to the explanation of Mulder&Scully back in action) and less to the dreams about the lost son.

    Moreover, is it just me or Duchovny still seems bored out of his mind? In the first episode maybe it was his way of acting as a “depressed” Mulder, but now…?