Mulder and Scully crawling out from underneath a bed.
Design by Abby Schreck

There’s an episode in the third season of “The X-Files” — “Quagmire” — where special agents Fox Mulder (David Duchovny, “Aquarius”) and Dana Scully (Gillian Anderson, “Sex Education”) are in Georgia investigating “Big Blue,” a continental version of the Loch Ness Monster. In the rest of the show’s “Monster of the Week” installments, there’s always something to hunt — a 200-year-old shapeshifting serial killer who lies dormant in 30-year increments, a human-flatworm hybrid that inhabits the New Jersey sewer system, a parasitic slug worshipped by a cult. But “Quagmire” is not so open-and-shut. 

Scully criticizes Mulder’s futile cryptozoological obsession, and she’s right. Mulder takes out an alligator instead of a water dinosaur. There is no Big Blue, and the two return to the FBI headquarters.

This isn’t entirely out of place, though. “The X-Files” waxes philosophical frequently, something that I missed as a preteen (admittedly, I was focused on the impossibly frustrating will-they-won’t-they dynamic between the leads). The show uses its Monster of the Week episodes to experiment — they are constantly stretching and contracting the ontology of monsters. Though inconsequential to the show as a whole, these episodes are fascinating explorations of the metaphysical.

Throughout “Quagmire,” though, Mulder is deadlocked on the existence of Big Blue. It’s a microcosm of his lifelong pursuit of the unknown — an obsession that is the very essence of his character, defining him as the foil to Scully’s voice of reason. A conversation near the end of the episode sums this up quite nicely. Scully compares Mulder to “Moby Dick’”s Captain Ahab, asserting that no matter what he believes, “everything takes on a warped significance to fit (Mulder’s) megalomaniacal cosmology.” She goes on, “It’s just … the truth or a white whale … what difference does it make?”

“The X-Files” exists in the realm of the uncertain, a story told through convoluted and inconsistent fragments from which we try to derive meaning. Its mythology is impossible to decipher under blankets of bureaucracy and government conspiracies. But Scully is a scientist through-and-through, here to pull back the curtains. “The X-Files”’ depiction of an even-keeled, astute and self-sufficient female scientist was state-of-the-art. When 13-year-old me met Dana Scully for the first time, I met myself. I learned that these aspects of her character — logic, calculation, perpetual skepticism — were the pieces making up my own view of the world. 

I wasn’t alone in this. Scully is responsible for a generation of STEM-interested women and girls, a theory that is not only supported by testimony, but a rigorous course of research, too — in true Scully fashion.  

But I never discussed how “Quagmire” ends. As the two walk away in defeat, the camera focuses on movement in the lake. The last shot of the episode captures Big Blue, crystal clear and glistening. It emerges from the mist before swimming away into the night.

Not only does Scully’s attack on Mulder discredit the very way he views the world, but she turns out to be wrong. Yes, Mulder tends to entertain the outlandish — his first impulse is to leap to some supernatural cause of that week’s unexplained events. That’s his schtick. But “The X-Files” is a show about monsters and aliens. So Mulder is almost always right. 

But still, how can Scully conclude that this “warped significance” Mulder applies to everything is strictly bogus? How can she say that it’s all for nothing?

Scully’s foundation of fact and pragmatism is riddled with fallacy. Her reductive thinking only muddies the waters because the true horror is the in-between — what lies in the expansive limbo between fact and supposed fiction. Mulder and Scully don’t know what they’re looking for half the time, and when they find it, the most they do is write up a case file and move on to the next. Their answers provide no clarity.

There is science in the world of “The X-Files,” but none of it fills the gaps. “The X-Files” does not exist in our universe — after all, Scully and Mulder’s world also has aliens, vampires, werewolves and mutant zombie viruses. And these things are tangible. Scully frequently uses her medical expertise to explain supernatural phenomena, like how mutant muscle tissue allows a person to shapeshift. But her textbook bible of natural science simply doesn’t include these things, so she dismisses them all — not by denying the possibility of existence, but by hitting a roadblock. To her, it’s not worth understanding, by carving out a new path of science or by contemplating the way these things fit into the world.

There’s an episode in season seven, “Hungry,” that switches the point of view from the special agents to the “monster” — a 20-something fast food employee who can’t stop eating human brains, but desperately tries to. By the end, he is entirely sympathetic. The presupposed meaning of a monster is out of one’s mind entirely.

“Hungry” introduces complexity to monsters, yet Scully puts off the ethical responsibility to treat them as such. That’s why at times it feels her devout scientism is tragically misplaced, because to her it’s all the same. It’s hard to think about how much she’s missing out on by lumping everything outside the natural sciences into a pile of drivel — and how much more she could explain with a mind wide open. She faces the very paradox she criticizes Mulder for — truth or white whale — and sees no difference, which is exactly the problem. 

Belief is not something to be litigated; it’s not a case of “you’re wrong, listen to me instead.” Scully doesn’t overtly dismiss all other schools of thought, but she lays out the groundwork for others to do so. Reckoning with this interpretation of Scully as a massive disappointment was like letting my younger self down. But my admiration for her still runs deep — Scully is half the reason I considered a career in forensic pathology, because she’s just that cool. Her brilliance significantly encouraged me to pursue a career in science, which isn’t going to change. At the very least, though, revisiting her flaws is an important exercise in recognizing and internalizing the limits of science for anyone involved in the field.

It’s attractive to always fall back on science — the real world doesn’t make a hell of a lot more sense than Scully’s universe. But we know that the unknown is scary. Embracing the feeling that there is so much more than what the eye can see requires that all disbelief is suspended. The things that can’t be explained should be confronted with uncertainty. That’s where “The X-Files” gets its monsters.

Digital Culture Beat Editor Laine Brotherton can be reached at