Content warning:  Sadly, to discuss how the show addresses Jackson’s conception involves talking about medical rape and other situations where our heroes suffer a loss of bodily autonomy. 

Note:  To clarify, I’ll be referring to William/Jackson by both names:  “William” will refer to the conceptual idea of William as an entity (whether that be absent son or tool of the conspiracy), as well as the actual infant, pre-adoption, and “Jackson” will refer to the person we now know him to be.

The X-Files’ 11th Season properly introduced us to Jackson Van De Kamp, last who we last saw in the flesh way back in 2002 as a baby named William Scully who had been given up for adoption for his own protection after going through a kidnapping, attempted murder, and multiple strangers trying to get their hands on him for one reason or another. As a baby, William exhibited signs of psychokinesis, where he had been shown to be able to control the mobile above his crib with his mind, as well as interact with an artifact taken from what appears to have been an alien craft found in Africa. As he grew older, William, now known as Jackson, continued to develop new, unexplained powers, and as of 2018, multiple parties were attempting to locate him in an attempt to use him for their own purposes.

But while it’s known that Jackson is not a normal child, the circumstances of how he came to be are still somewhat unclear. He was born to Dana Scully (theoretically circa early 2001 or possibly very late 2000, depending on how you choose to unravel the muddled pregnancy timeline) and was given up for adoption before his first birthday (possibly at around 10 months old, though again, the timeline is murky at best). Of course, Dana Scully was diagnosed with infertility after her abduction in 1994, where seemingly all of her ova were taken from her. She had attempted IVF using some of her recovered ova along with Mulder’s sperm, but this was apparently unsuccessful. At some point shortly before discovering that she had become pregnant in mid-May of 2000, she had both suffered an unspecified violation at the hands of the Cigarette Smoking Man while traveling with him and had sexual intercourse with Fox Mulder on at least one occasion.

Once William was born, Scully and Mulder considered him their child and continued to do so throughout the series up through Season 11. In 2018, the Cigarette Smoking Man claimed responsibility for his creation. Jackson acknowledges that Scully is likely his biological mother based on their shared psychic bond but has doubts that Mulder is his father based on their lack of psychic connection. He acknowledges that CSM is likely his father (either figuratively or literally) due to the visions he’s had, though it’s never specified whether or not there’s any kind of literal connection between them like he has with Scully.

But what’s the truth of the situation? Even in the end, it remains unclear. Between truth and lies, hope and fact, the pieces of the puzzle can be arranged in multiple configurations. In the past, Season 2 – 9 mythology co-writer Frank Spotnitz has stated plainly that Mulder is William’s father. In Chris Carter’s commentary for the series final episode, My Struggle IV, he suggests that Mulder is not Jackson’s biological father due to the fact that Mulder doesn’t share his visions the way Scully does. CSM claims to be the father, but in an episode whose tagline reads “I Want to Lie.” Who and what do we believe?

It’s entirely possible that the plan for William/Jackson’s origin had changed between the original series finale in 2002 and where we stand now in 2018. And it’s possible that it could change again if the series continues on in any form, whatever Carter’s intentions may be now. The pieces have all been set up for years, but their arrangement may simply twist and turn into whatever will make the most compelling story.

So, here we are at the end of the series as we know it, with the information laid out for us in the show still as incomplete and unreliable as ever. And maybe the truth we can’t know. So, then… what are the possibilities?

The Players

We know Dana Scully is Jackson’s mother, but who is his father? Is it Mulder, as they’d presumed for years? CSM as he’s claimed and appears to believe? Or something far less human? Let’s take a look at our heroes and villains and consider how their unique history could have resulted in a child with such unusual abilities.

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Dana Scully

• We know that Scully is William’s biological mother due to the DNA tests that were run in Ghouli using Scully’s cheek swab and Jackson’s hair. Mulder gets the test results and implies a positive match when he tells Scully “it’s not good news” and then also confirms it again when he’s talking to Skinner. [Note: There’s been some confusion around Scully’s line in My Struggle IV where she says, “I carried him, and I bore him, but I was never a mother to him.” Some have taken this to mean that Scully is not his biological mother, but she is most likely just reflecting on the fact that she didn’t get to raise him, as we know she is his biological mother from the DNA test. If he had been an experiment, it was likely that his creators (and others who wanted him) had always intended to take him from her (as we saw some evidence of in Season 9), preventing her from raising him to adulthood. And in her own sacrifice, hiding him to protect him, he would never know her as his mother, anyway, being raised by another couple.]
• Scully has manufactured alien DNA resulting from her abduction, but was also exposed to the alien virus via bee sting, had god knows what done to her in Antarctica, and was given the vaccine. She also has a chip in her neck that, whatever its purpose, is capable of affecting her on a biological level.
• Scully’s alien DNA was again confirmed when she sequenced her genome in My Struggle.
• During her abduction, Scully’s ova were harvested and used in experiments to create alien-human hybrids. Emily was the result of one of these experiments.
• When she attempted in vitro fertilization, the doctor performing the procedure was affiliated with the conspirators trying to create alien-human hybrids.
• After she became pregnant, she also continued to see these doctors during the first part of her pregnancy, potentially giving them access to make alterations to her body and the fetus.
• Scully became sexually involved with Mulder within the same general timeframe as when CSM claimed to impregnate her.

Fox Mulder

• Mulder was sexually involved with Scully around the time that she became pregnant.
• Mulder had been infected with the Black Oil while in Tunguska and was given an experimental Russian vaccine for the alien virus.
• Mulder developed the ability to read minds and anticipate near-future events after being exposed to a rubbing from an alien craft. The rubbing would have contained traces of cosmic galactic radiation, which were present in the alien artifact. Michael Kritschgau explained that the alien virus had been reactivated in him by exposure to an alien source of energy (presumably the CGR contained in the rubbing).
• Mulder’s abnormal brain activity in the Biogenesis trilogy is similar to what we see in Scully’s brain scans in My Struggle III after she starts having her seizures/visions.
• One of the Project doctors describes Mulder as a “compatible alien-human hybrid,” a ready-made version of what their scientists had been trying to create for so many years.
• CSM mentions that, in this state, Mulder would be immune to the coming viral apocalypse.
• CSM removes genetic material from Mulder’s temporal lobe associated with his ability to read minds and anticipate the future, as once it is removed, he no longer has those abilities.
• While it was believed that Mulder had made a full recovery from this non-consensual brain surgery, he apparently continued to experience irregular brain activity, which grew worse over time.  It’s possible that his alien DNA may have continued to affect other parts of his brain even after the genetic material in his temporal lobe that allowed him to read minds was removed.
• It was most likely some point after his exposure to the alien artifact that Mulder agreed to be the sperm donor for Scully’s in vitro fertilization attempt, where Mulder unknowingly handed his alien-human hybrid sperm right over to the Project doctors. Oops.
• It was after William’s conception that Mulder was abducted, tortured/experimented on, left for dead for three months with an alien virus (a different one?) brewing inside him, and then revived after Scully administered courses of transfusions and antivirals, so it’s unclear exactly how his physiology may differ now compared to when William was conceived. This may explain how he could have gone from being supposedly immune to the viral apocalypse to being a potential victim in Scully’s vision.

Cigarette Smoking Man

• While CSM had no problem performing experiments related to the Project on various family members, there’s no indication that he had done any on himself until 1999, when he stole alien-activated genetic material from Mulder’s brain and inserted it to his own in an attempt to become an alien-human hybrid himself and therefore be immune to the viral apocalypse.
• It’s unclear how successful the surgery was. In En Ami, he tells Scully that he’s dying of cerebral inflammation as a consequence of the surgery, which was similar to what Mulder was experiencing. Unlike Mulder, though, by the end of the seventh season, CSM is looking a lot worse for the wear, having since received a tracheotomy, and now also bound to a wheelchair. Though of course, it’s possible that age and other health conditions (*cough*smoking*cough*) may have hastened his decline.
• Also in En Ami, CSM is alone with Scully after she passes out, and this is where we get into horrible medical rape territory. In My Struggle III, CSM reveals to Skinner that he had impregnated Scully (“with science,” according to Chris Carter) during their time together. It remains unclear if she was literally impregnated (had a fertilized egg/fetus implanted), or if her fertility had been restored somehow via the chip in her neck, giving her the ability to reproduce naturally, or something else entirely. Altering her chip seems most feasible for one man who is not a doctor or scientist, but who knows, maybe he keeps a team of doctors on call out in the woods.  *sigh*
• CSM refers to William/Jackson as his “son,” but he also calls himself his “creator.” It’s unclear if William/Jackson is CSM’s “son” in a literal, biological sense, using his own DNA, or if he is simply just the product of an experiment that CSM had engineered using other human and/or alien DNA. And it’s also unclear if any of this is actually true at all, as CSM is a goddamn liar.
• Whatever potential alien abilities CSM may have gained by taking Mulder’s alien-activated genetic material is also unclear. He doesn’t seem to have gained the ability to read minds, as if he had, he’d have known about Krycek and Marita’s plans to betray him in Requiem, Monica’s ulterior motives to warn/help Scully and Mulder in My Struggle IV (and likely before that), and especially that the person he shot on the pier was Jackson and not Mulder.
• Does he have the ability to see visions like Jackson and Scully? Is there any connection there? This is also unclear. We’re not given any definitive evidence that he does, but we’re not given evidence that he doesn’t, either, outside of it not actually being shown or mentioned. Could these visions be why he thinks he’ll need to kill Mulder, because he sees visions of Mulder killing him? Could it be why he tells Reyes that Jackson is in danger, but he does’t quite understand from whom? But on the other hand, he’s always kept tabs on everyone important to his plans and has other channels of information, as we see how easily he’s tapped Jeffrey Spender’s phone, for example.
• Jackson does acknowledge CSM as his father and wonder why, if Mulder claims to be his father, Mulder doesn’t see the visions like Scully does. But does this imply that CSM does see them, or does Jackson not actually know, not haven spoken to CSM directly? Is this purely a bond between mother and son, as Reyes seems to imply in My Struggle III? Jackson may acknowledge CSM as his father simply because he’s claimed it to be so, and Jackson can see that in his visions. Would Mulder even have the capacity to receive these visions after CSM took genetic material from the part of his brain that allowed him to hear thoughts and anticipate the future? If CSM does receive visions, is it only because he took that genetic material directly from Mulder?
• Is CSM still alive because his brain surgery with Mulder actually allowed him to become an alien-human hybrid with the ability to heal himself? Could something he’d found in the Anasazi ruins where he’d been hiding out in Season 9 have activated the genetic material taken from Mulder in the same way that it was activated in Mulder by the radiation from the rubbing? The magnetite in the ruins supposedly keeps it safe from the aliens, who fear it, but it’s also supposedly responsible for downing alien crafts.
• CSM also briefly had access to a disk supposedly containing the cure for all human disease, which was largely extraterrestrial in nature. He appears to toss the disk into a lake, supposedly not utilizing its contents, though who knows if the disk or the information on it could have at some point been recovered.

William/Jackson

• Jackson’s psychiatrist tells Scully that he had symptoms that coincide with extreme electrical activity in the brain, similar to Scully in My Struggle III and Mulder in the Biogenesis arc.
• Jackson is able to share his visions with Scully, and she’s the only person he mentions being able to share them with in Ghouli. It’s unclear if he has this link with anyone else.
• Reyes says to CSM in My Struggle III, “Scully and her boy have a bond beyond you, beyond science.”  CSM says that Scully is completely unaware of it, which Reyes questions, and CSM replies “It’s a secret only you and I know.” Does this refer to their shared visions, or something else?
• The full extent of Jackson’s power is still unknown. In addition to having potential visions of the future, Jackson can project images to others to make either himself or someone else appear to be someone or something they’re not. He seems to be able to affect electrical currents somehow, changing traffic lights or radio stations with his mind.
• It’s unclear whether or not he can read minds in any capacity. He has suspicions about some of the people he comes across, though he may be getting flashes of possible futures. He knows that Mulder is CSM’s first born son, but how did he obtain this information? Could it have been from a vision where CSM reveals this? Does he have any control over the visions he has, and does he know whether or not they may be accurate or if they can be changed?
• Jackson survives a gunshot to the head, implying that he has regenerative abilities. Does he also have the power to heal others, as we’ve seen with Jeremiah Smith and the Alien Bounty Hunter? In one of his childhood flashbacks, we do see him showing off a chick hatching from an egg in his hand, which could imply life-giving or life-restoring powers of some sort.

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Conception Scenarios

So, with their history in mind, what are the possible circumstances surrounding William/Jackson’s conception, and how likely are each of these scenarios in the context of the show?

Miracle of Nature
In this scenario, William is conceived naturally via intercourse between Scully and Mulder without any outside intervention. By some miracle, Scully still has a few surviving ova to make this possible. Any abilities that William has are a result of the combination of his parents’ uniquely altered DNA.

At this point, this seems a bit unlikely considering the focus on him being an experiment, but not out of the realm of extreme possibility, especially in light of Scully’s second pregnancy with no apparent outside tampering.

Miracle of God
Immaculate conception, or perhaps an answered prayer for Scully and Mulder after the failed IVF? (“Never give up on a miracle.”)  This also doesn’t line up so well with the focus on experimentation. however, there were a LOT of religious undertones and imagery in Seasons 7 and 8, which makes it all fair game. The implication that what humans consider to be God is of alien origin also plays into this theory.

And of course there’s all of the Saint Rachel references in relation to pregnancy #2 in Plus One… (Here’s hoping Carter doesn’t take that story too literally, though.)

Experiment – Half Alien
In this scenario, William is literally half human and half alien, without any human biological father to speak of. This would mean that all of William’s human DNA would come from Scully and any remaining DNA would be extraterrestrial in origin. In Essence, Lizzie Gill admits to such experiments taking place, “We were surprisingly successful with a clone from a human egg and alien DNA. DNA that the government had since 1947.” This seems to be, theoretically, how hybrids such as Emily were created. The challenge to this theory, however, is that unlike Emily, William is male, and Scully would have no Y chromosome to pass on to produce a male offspring.

Experiment – CSM’s Biological Child
This seems to be the general stomach-turning consensus after CSM’s revelation in My Struggle III and follow-up in My Struggle IV. CSM is a sadistic, egotistical liar, which made his claims questionable in My Struggle III, but Jackson seeing him as his father in visions then gave those claims some possible credibility in My Struggle IV. As mentioned above, it’s still unclear whether CSM was able to share visions with Jackson the way Scully was, but if he can, he would likely also be experiencing anomalyous brain activity and have some element of alien-activated DNA (and having alien DNA from both human parents would seem to make sense for a human child with strong alien abilities). Now, one would probably assume that CSM must have some degree of alien DNA in order to somehow recover from having his face blown off by a missile, but where did that come from? From what we’ve actually seen on the show, the answer would be: Mulder.

When Mulder gained the ability to read minds after being exposed to both the Black Oil and rubbings from the alien ship, the Project doctor stated to CSM, “It’s a chance none of us ever expected… let alone hoped for. After all these years trying to develop a compatible alien-human hybrid and to have one ready-made.” At this point, in addition to reading minds, Mulder exhibited the potential for limited future sight, and he was thought to be immune to to the coming viral apocalypse. In wanting to take these traits for himself, and taking advantage of his biological paternity to Mulder potentially allowing for genetic compatibility, CSM had the project doctors literally remove genetic material from Mulder’s brain and put it into CSM’s, after which Mulder loses the ability to read minds, and CSM seems to gain the ability to cheat death.  

So, in this sense, if Jackson received alien-activated DNA from CSM, it could also mean that genetic material originally came from Mulder, making both of them his fathers, in a sense. Which sounds like some creepy Peacock family shit when you think that Mulder could potentially be both Jackson’s brother and father, in a sense, but also slightly less creepy from Scully’s point of view in a way, since at least her child could be partially Mulder’s.

Experiment – Mulder’s Biological Child
But while it’s possible that CSM could have used his own sperm to create a child, it’s also not out of the question that he could have used Mulder’s. Mulder did, after all, hand his sperm right over to the Project doctors during Scully’s IVF attempts in Per Manum, and his status as a “ready-made” alien-human hybrid would likely make him a good candidate to use for these experiments.

CSM could have also used Mulder’s sperm in his own twisted take on philanthropy. He was likely aware of the failed IVF attempt and had a strange soft spot for Mulder and Scully, despite the horrors he subjected them to over the years. By impregnating Scully with Mulder’s sperm, he could have seen it as giving them something they wanted while still furthering his own goals. He could be a god, creating a possible savior for humanity, and it would also be his biological grandchild, which would still further his personal legacy.

So, if Mulder could be Jackson’s biological father, why, as Jackson asks, can’t he see the visions? While Mulder did exhibit abnormal brain activity similar to Scully and Jackson in the past, the part of his brain that was used to read minds and anticipate the future appears to be what CSM removed from him and put into himself in Amor Fati. That could be one potential reason, if Mulder actually was Jackson’s father, that Jackson might mistake it for being CSM. Though the nonconsensual brain surgery happened prior to conception, Mulder continued to experience other anomalous brain activity up until he was revived from the dead via Scully’s transfusion and antiviral cocktail, which may have diminished any remaining alien traits.

Experiment – Some Other Dude’s Biological Child
I guess some random guy’s DNA could have been used in the experiment, but that’s pretty boring and discounts a father with potential alien DNA to combine with Scully’s, unless it was someone else who had been through similar experiences (insert Krycek-as-Jackson’s-father fan theories here).

Medical Implantation
So, paternity options aside, how did Scully actually become pregnant? If Scully was, in fact, “impregnated by science,” what does that actually mean?

If an embryo had been created in a lab, it would likely need to be implanted somehow. This is one possible scenario for the unspecified violation Scully experienced in En Ami. All we know is that she passed out in the car, and woke up in a strange bed in different clothes. It’s unclear exactly how much time had passed.

Could an embryo have been implanted without her knowledge while she was passed out? Who would have done it? In the episode as it originally aired, CSM appeared to be alone with Scully in the house, telling her that he carried her inside. In My Struggle III, the dialogue was for some reason altered to imply that an unseen housekeeper was also present. Could this mysteriously appearing “houssekeeper” be a doctor? It seems highly unlikely that CSM would be implanting any embryos on his own. This seems to be the most obvious retcon in relation to this plotline.

Experimentation After Conception
In any of these scenarios, but especially going back to “Miracle of Nature,” it’s possible that conception occurred naturally, but then changes were made to the fetus in the womb that resulted in Jackson’s powers. Since Scully continued to see the same doctors she used for her IFV during the first part of her pregnancy, and we know they were affiliated with the Project (likely “Project Crossroads,” as it’s come to be known in Season 11), it’s possible that experiments could have been done on her without her knowledge during her check-ups.

This seems like one of the less likely scenarios, however, as while the Project was likely involved during this stage, it seems more likely that they would simply be doing tests and monitoring the mystery pregnancy rather than actively making changes to the fetus.

Fertility Restored by Alien Ship
This is an older theory that side-steps the experiment angle. The theory here is that when Scully came in contact with the alien ship in Biogenesis/The Sixth Extinction, her fertility was restored, similar to how the power of the ship could bring dead fish back to life. After this happens, then natural conception via intercourse once again becomes possible.

Again, this doesn’t really line up with the experiment angle if we’re to believe that one, but it’s another one that could explain Scully’s second pregnancy so many years later.

Fertility Restored by Chip, Artificial Conception
Another theory that remains popular is that Scully’s fertility was restored by a modification to the chip in the back of her neck, just as it was used to cure her cancer. This theory works thematically with the plot of En Ami, where alien-derived science is used for things like curing disease and extending life and is administered via a chip inserted in the back of the neck. Swapping or modifying Scully’s chip seems like a slightly less invasive and therefore less noticeable thing to subject Scully to as she’s passed out compared to implanting an embryo, and something that CSM could potentially administer on his own without a team of doctors swooping in.

Once fertility is restored, however that may be accomplished, the question is still then how does conception occur? In going with the half-alien theory, it’s possible that the chip could have triggered an egg to be created and modified using Scully’s own native DNA mixed with the alien DNA present in her body since her abduction. It still doesn’t quite explain where the Y chromosome came from, but hey, maybe the chip can somehow construct one with tiny nanomachines, I don’t know.

Fertility Restored by Chip, Natural Conception
And probably the fan favorite theory is that the chip restored her fertility somehow using alien science, but William was then conceived naturally via sexual intercourse a couple of weeks later.

I think this one resonates with people because it strikes a nice balance between alien and human, technology and love. It acknowledges both the godlike intervention of CSM, and the powerful love between Scully and Mulder. It’s a loss of bodily autonomy in one respect, but an expression of  consensual intimacy in another.

And if William was conceived naturally between two humans who had already been genetically modified by their exposure to the alien virus and vaccine and the other things they’d been subjected to over the years, that may be a possible implication as to why William succeeded where others had failed. Again, Lizzie Gill says to Mulder, “The child she is carrying is very special. One could only hope to create that in a lab. A perfect human child but with no human frailties.” This seems to imply that she believes that he wasn’t necessarily created in a lab, but was possibly a miracle combination of genetics that hadn’t been planned for.