A Theory About Mulder and Scully’s Son on The X-Files

By  · Published on January 28th, 2016

The second episode of The X-Files revival, which, as I said yesterday, was a vast improvement upon the first, also answered some burning questions from the first episode. Namely, what happened to William, Scully and Mulder’s son? For those uninitiated to The X-Files, the existence of William was something they learned for the first time; the minds of new fans are blank slates where the original series’ mythos is concerned. All they knew was that Mulder and Scully had a son, that his name was William, and that, for whatever reason, they’d lost him. Was he dead? This seemed the most likely answer, given how they spoke of him in the past tense.

But episode two, “Founder’s Mutation,” blew that wide open as we were given a glimpse of just what had happened to their son. In a series of two separate flashbacks, one each from Scully and Mulder, William’s story was told. They had raised their son in until he was in his pre-teen years, memories of each of them sharing loving, wholly normal moments with William: taking him to school, building a rocket. But, being the result of a genetic experiment done upon Scully while she was pregnant, had hybrid human-alien DNA and the effects started to manifest themselves as he reached puberty in dangerous ways: black, pupil-less eyes suddenly peering out from his frightened face, levitating over his bed as what appeared to be a ray from an alien spacecraft trapped him, inspected him. So he was sent away for his own safety.

Longtime fans of the show, however, were left scratching their heads, as William’s story had clearly been rewritten. In the last season of the original run, after William started to manifest his powers early on, Scully decided it was best for her son if she were to give him up for adoption so neither the government nor aliens could find him. The infant was adopted by the Van De Kamps, and the 2008 movie, The X-Files: I Want to Believe, once again confirmed that Scully and Mulder no longer had their son.

So how did the two suddenly regain custody of their son and raise him for ten more years between then and now?

The answer is… they didn’t.

Now, hear me out here, because I have a theory. The interludes with William weren’t flashbacks of memories, but daydreams ‐ and then nightmares. And I’m aware that this might all get blown to hell in the very next episode, but for now, it’s a theory that just feels right, somewhere deep in my gut. Sometimes that happens. At some point, in between the vast conspiracy theories and mutant, X-Men-like kids with psychic abilities, “Founder’s Mutation” quietly became the most human X-Files episode of them all.

The key that these moments never happened in reality can be found in the nightmares of each. For Scully, whose life has been irrevocably altered by her abduction while pregnant and genetic tampering, her greatest fear is how that might manifest itself in her own son. And it’s understandable it would be on her mind even more heavily than usual, having just learned in the previous episode that she, too, now possesses alien DNA. For the rational, logical, always-in-control Dana Scully to have something so irrevocably horrifying happen to her in a manner that is completely outside her control or consent, it is the ultimate nightmare. Her mind, half-mother, half-medical scientist, would understandably project its deepest fears in something rooted in concrete biology: how her son’s hybrid DNA might manifest itself in him, physically, mentally, make him a freak or object of fear.

Mulder’s nightmare scenario for his son was also uniquely personal to him and, like Scully’s did, took the form of his own deepest fear. Fox Mulder’s life has been forever shaped, for better or for worse, by the abduction of his sister, Samantha, when he was only twelve. It was an event that he saw with his own eyes: the flashing strobes, the blinding ray of light, the levitation, the eerie hum. Samantha’s abduction has been the singular event of Mulder’s life, the one that continues to haunt him and drive him to this day. It’s what pushed him into his obsessive pursuit of the truth, because for Mulder, it wasn’t simply the abduction that affected him so deeply, but the fact he never got answers, never found closure ‐ and that he was powerless to stop it. His son being suddenly abducted in the same way, and worse, for Mulder to witness it and once again be unable to stop it, would be the scenario that terrified Mulder most in this world.

Essentially, these interludes were not Mulder and Scully reliving the most painful moments of their lives, but trying to rationalize away their guilt by imagining what might have happened had they been selfish and kept William with them, had they not sent him away to keep him safe. Rationalizing that it was for the best is the only thing that they can do, not as logical FBI agents, but as grief-stricken parents who have lost their son.

Even their happier daydreams of what might have been hold seeds of their individual fears. For Scully, the act of taking her son to school and then letting him play with friends ends in a medical emergency when he’s in an accident and his arm is broken ‐ once again, the doctor’s mind projecting her fears, however reality-based, of her son’s body being damaged, imperfect, invaded. Mulder’s daydream of an idyllic evening setting off bottle rockets with William and igniting his passion for space is marred with a single line. “I’m gonna go up there someday,” says William, gazing up at the sky. It’s a prescient bit of foreshadowing for the very next scene, but more than that, it’s a manifestation of Mulder’s deep fear of his son indeed going “up there,” but against his will and to terrible consequences.

Next: The X-Files Return Was a Mess, But It’s Nice to Have It Back

Mulder and Scully have had a long and strange relationship. Though they clearly have deep love for one another, their romantic relationship has largely happened off-screen, only being implied or referenced the vast majority of the time. So much of the depth of their relationship has been built not in what we see, but in what we don’t see ‐ or hear. Much of what passes between them is in what’s left unsaid, in shared looks, not words. “Founder’s Mutation” was, in The X-Files’ own roundabout way, not an episode about Scully and Mulder, agents investigating a case, but Scully and Mulder, parents. In the years the series has run, it was the most revealing episode yet regarding the personal life that the two had shared together, as well as an unflinching examination of all that had ultimately driven them apart. As a human truth wrapped in an enigma, it worked.

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