The X-Files: Complete Guide to the Mythology

The X-Files revival extended trailer

It’s safe to say that The X-Files has one of, if not the, most complicated narratives told in the television format, partially a consequence of its running for nine seasons (and two feature films) and partially the direct result of creator/showrunner Chris Carter’s deliberate, convoluted storytelling methodology; the executive producer has said many dozens of times over the years that, had he just laid out the whole mythology of the series in one sweeping gesture, it would be too fantastical to be believed.

But this is exactly what we’re going to do here; it’s all well and good to have half-truths and redactions and obfuscations at nearly every turn for 201 episodes, but when attempting to bone up before the show’s grand return to television this weekend, it’s necessary to have that straightforward, step-by-step summation made available.

So, without further ado, here is our Complete Guide to The X-Files’s Mythology. (And once you’re done here, be sure to check out our top 10 reasons why we’re worried about how this storyline may be picked up – or not – in the revival series.)

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10 In the beginning…

Biogenesis - Complete Guide to The X-Files's Mythology

The building blocks of life may have arrived on Earth thanks to a meteorite (probably originating from Mars), but it was a race of extraterrestrials that made mankind into what it is today – a series of UFOs arrived on the planet millions of years ago, covered in verses that would eventually find their way into all of man’s various religious texts and written in a language that would ultimately reemerge as a Native American dialect. It would seem that the aliens shaped man more or less into their image physically, as well, although evolution would take its course, turning off most of the aliens’ physiology and rendering it into what scientists now call junk DNA. (Occasionally, a human is born with at least some of this DNA activated, giving him such abilities as telepathy; the series refers to these individuals as being “more human than human.”) It remains unknown why these extraterrestrials created humanity or whether they’re responsible for other civilizations on other planets, as well.

Also arriving on that meteorite was an already-evolved lifeform, an alien virus that has since come to be called Purity. This virus is sentient and is able to function by invading a host species and transforming it into an alternate, perhaps more ideal (for defensive purposes) form. Purity flourished as the original inhabit of the planet until the next ice age began; extreme cold is one of the virus’s few weaknesses, and it was forced to abandon all of its various hosts and travel deep underground, where it eventually hitched another ride – this time within oil, another medium that can be perfectly manipulated (hence Purity’s nicknames as the Black Oil or the Black Cancer throughout the show).

9 The aliens become infected

The two opposing alien factions - Complete Guide to The X-Files's Mythology

It is unknown whether the alien race was present on Earth along with their early vessels, but, at some point, they came into contact with Purity and became almost entirely subsumed by it. It seems that the two lifeforms evolved into symbiotic partners, with the aliens becoming Purity’s permanent hosts and Purity becoming the main reproductive method for the aliens (a host is infected and then used as an incubator for the alien offspring, which consumes the host’s body when it is birthed).

It is at this stage that humanity is viewed as the perfect crop to be harvested, and plans are made to return to Earth – presumably once the ice age retreats – to reclaim it. In the meantime, the newly reconstituted aliens colonize as many other planets in the cosmos as possible, spreading the virus and strengthening their ranks. Only a small number of these so-called alien colonists (at least, so far as we know) manage to resist infection, using their latent shape-shifting abilities to seal off every body orifice to prevent Purity from entering their systems. These alien rebels make it their life’s work to halt the spread of the virus everywhere they can across the galaxy – including, eventually, Earth.

8 The birth of the Syndicate

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The alien colonists make their long-awaited return to Earth in the 1940s, where they encounter a (comparatively) technologically advanced human species. Several of their ships are unexpectedly downed when they are exposed to deposits of magnetite, a mineral that is toxic to them and which apparently also arrived on the planet thanks to that fateful original meteorite.

The State Department is sent to investigate this new extraterrestrial presence – including, most importantly, what their intent to humanity is – and to keep its existence a secret from the general public, which the American government agreed to do along with all the other leaders of the world in order to prevent a global hysteria. Eventually, after 26 years of investigation, the top-secret group within State pieced together the colonization project and realized that they had no hope of preventing its commencement. Instead, they made a bargain with the aliens: in exchange for them not launching a series of nukes and plunging the planet into another ice age, they and their families would be spared the viral apocalypse. In return, the government agents pledged to lay the groundwork for the invasion and to ensure that everything transpires as smoothly as possible. In this way, the project originally contained within the American government quietly became a global Syndicate.

What neither side realized was that each had a secret. The alien colonists allowed their human collaborates to believe that Purity would transform all of humanity into mind-controlled zombies instead of being fodder for their reproduction. For their part, the Syndicate labored to create a vaccine to Purity, to stave off the colonization altogether (or, at least, to ensure their own safety).

7 Enter the X-files

Mulder and CGB Spender - Complete Guide to The X-Files's Mythology

In 1952, Special Agent Arthur Dales (Darren McGaven) becomes entangled with Bill Mulder (Peter Donat), Fox’s (David Duchovny) father and a secret member of the Syndicate, and thereafter becomes obsessed with cases with an extraterrestrial or otherwise paranormal bent, thereby officially birthing the X-files unit. (Why X? Because the FBI’s secretary filed them in the “X” drawer after the “U” drawer [for “unsolved”] became too full.)

When Dales retires years later, the FBI hierarchy is only too happy to have the X-files shut down – until Agent Fox Mulder, hugely successful as a psychological profiler and with contacts in both the Senate and the State Department (thanks to his father), is able to use his sway to reopen them. His overriding goal: to locate his sister, Samantha, who was abducted by aliens in 1973, and to blow wide open the government conspiracy of silence regarding extraterrestrial life on Earth (much to the Syndicate’s chagrin). His initial partner is Agent Diana Fowley (Mimi Rogers), his wife at the time, though both their marriage and partnership fell apart shortly thereafter.

To replace her, the Cigarette Smoking Man (William B. Davis), a member of the Syndicate whose plate of responsibilities includes keeping all of the various agencies housed in Washington, DC in line, recruits Dana Scully (Gillian Anderson), a medical doctor well-trained in the scientific method – and a firm non-believer in the supernatural. It is Cancer Man’s hopes that Scully’s skepticism will infect and undermine Mulder’s quest for the truth, ultimately deterring it (and preventing the Cigarette Smoking Man from having to kill him, which runs the danger of turning one man’s crusade into a full-blown movement).

6 The Mulder and Scully years

Gillian Anderson and David Duchovny returning for The X-Files revival

From March 1992 to May 2000, Mulder and Scully investigate hundreds of X-files and slowly, irrevocably work their way to the truth surrounding both the Syndicate and the alien colonists. Along the way, they pick up several insider sources from the very heart of the government conspiracy, who help point the agents in the right direction – and who inadvertently help cause the X-files office to be shuttered two additional times, as Mulder and Scully’s continued successes make them ever-more-dangerous to the colonization project. Both times, however, forces from within the FBI – including Assistant Director Walter Skinner (Mitch Pileggi), the agents’ supervisor, who, despite his own skepticism, secretly admires their willingness to ask questions that no one else will – intercede and eventually get the X-files back on track.

At one point, exasperated by his inability to thwart Mulder, the Cigarette-Smoking Man arranges for Scully to be made part of the Syndicate’s project by becoming an alien abductee (more on this in a moment). Although she is only gone for several weeks, the damage done to her in the wake of the experiments is immense: her ova are confiscated, resulting in her infertility, and she is given a microchip implant at the base of her neck. When Scully detects this and has it removed, she develops a lethal form of brain cancer which threatens to kill her within the space of just a few months – a failsafe that the Syndicate’s doctors install into each of their test subjects in case they remove the microchips. Scully is only able to survive due to Mulder’s procuring of an antidote that the Syndicate has developed (namely, inserting a new implant), but her inability to have children haunts her for the duration of the series.

5 The Syndicate’s destruction – and Samantha’s discovery

Through its many decades of operation, the Syndicate’s overriding project is the creation of the perfect human-alien hybrid, which would be impervious to infection from Purity and which could be genetically manipulated to be a race of mindless slaves once colonization is complete (the Syndicate and its chosen family members would be injected with the hybrids’ DNA, granting them immunity from the alien virus). It is for this reason that thousands of innocents are abducted and experimented on, and it’s the Syndicate’s own loved ones who start the process in 1973: as a sign of good will, they are handed over to the colonists to be the first abductees. Bill Mulder chooses his daughter, Samantha; CGB Spender – better known as the Cigarette Smoking Man – hands over his wife, Cassandra (Veronica Cartwright).

Although deliberately dragging their feet on the hybrid experimentation, the Syndicate successfully transforms Cassandra Spender into the first perfect hybrid in early 1999, which moves the start of colonization from its drop-dead date of December 22, 2012 to that very day. The alien rebels (who have finally reached Earth), however, act first, seeking to turn the Syndicate from its self-preserving ways; when they fail, they instead gather up all of its members – save for CGB Spender, of course – and kill them. The Syndicate and, perhaps, the colonization project seem to be dead.

So, too, unfortunately, is Samantha, a fact which Mulder is finally able to track down in early 2000. Given that the Cigarette Smoking Man is really both her and Mulder’s father – Mulder’s mother, Teena (Rebecca Toolan), had a long-lived affair with the villainous chain-smoker – she was returned to him instead of the Mulder family. She spent the rest of her short life being the repeated test subject of additional, horrific experiments at Spender’s hand, until 1987, when she is spared the suffering by a merciful and timely death.

4 The new alien conspiracy

With their human co-conspirators removed from the picture, the alien colonists revert to their pre-determined December 2012 date and move to replace their terrestrial allies in positions of power all across the planet with a brand-new type of human-alien hybrid: the human replacement or alien replicant (or the “super soldier,” as their cover story names them). Re-abducting the previous test subjects all throughout the year 2000, the colonists infect them with a new type of virus that replaces the host with a near-identical copy but which is incredibly strong (the replicants can decapitate someone with one swipe of their hands) and nearly impossible to kill (a metallic spine can regenerate itself and then all other tissues).

Mulder is nervous that Scully, given her previous history as an abductee, would be put on the colonists’ list, but it’s actually Mulder that they want – throughout their years on the X-files, Mulder is inadvertently exposed to a whole series of alien contagions and sources of radiation which have the net effect of altering his brain chemistry to that of a perfect human-alien hybrid (even going so far as to make him temporarily telepathic). Although CGB Spender performs an operation on Mulder that reverts his brain chemistry back to normal – and enables Spender to inject Mulder’s “hybrid” DNA into his own body, thereby granting him immunity from Purity – he’s still the best candidate that the aliens have access to.

Mulder himself is abducted in May 2000 and goes missing for nearly a year. During that time, the FBI hierarchy sees an opportunity to insert one of their own into the X-files office and, they hope, begin the surreptitious process of shutting it down. That new agent is named John Doggett (Robert Patrick), a skeptic, who gets temporarily partnered with a Scully who, after eight years of investigating the paranormal, has finally seen enough to become a believer. (What they don’t count on is Doggett’s integrity and his genuine curiosity at solving these impossible cases, making him a worthy successor to Fox Mulder.)

3 Scully’s miraculous conception – and birth

Scully pregnant - Complete Guide to The X-Files's Mythology

Immediately after Mulder’s disappearance, Scully receives another shocking bit of news: she’s pregnant.

The nature of her conception is a driving mystery throughout The X-Files’s final two seasons. While it’s revealed that she had quietly been undergoing fertility treatments – and that she even asked Mulder to be her donor – audiences are also led to believe that the two finally bit the bullet and spent the night together, even though neither one is brave enough to acknowledge the event, and they keep acting as if nothing has changed between them. The most likely explanation, however, would seem to be yet another repercussion from Scully’s abduction back in 1994: her conception was triggered by another variation on the human-alien hybrid project, which the alien colonists have taken over and resurrected. A number of female abductees have suddenly, miraculously given birth, and each of their babies has demonstrated “more human than human” abilities, such as telekinesis; Scully’s son, whom she names William, even manages to interact with an UFO, proving his extraterrestrial origin.

Since it is believed that this new race of human replacements would be the leaders of the colonization that is scheduled to occur 11 years after their births, William’s life is constantly in danger, both by those who wish to keep him from Mulder’s anti-authoritarian influence and those who wish to stop the alien invasion by any means necessary. Finally, at the very end of the series, little William is injected with magnetite, which destroys the alien part of his hybrid DNA, and Scully, fearful that the pro-colonization forces will now kill her son out of pure spite, gives him up for adoption. The choice ensures the baby’s safety, but it also incessantly hangs over Scully.

2 The Doggett years

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Special Agents John Doggett and Dana Scully head up the X-files for nearly a year, from May 2000 to early 2001, with locating Agent Mulder forming their primary task. And even after Mulder is returned in the spring of 2001, Doggett remains the supervisory agent of the X-files – particularly after Mulder finally goes one step too far and gives his superiors the justification they need to fire him. (Why doesn’t Mulder shed his skin and transform into a human replacement? Because Scully is able to successfully create an antidote that permanently cures him of both the new alien virus and the lingering effects of his hybrid brain chemistry.) Although initially suspicious of the “career boy” Doggett, Mulder comes to realize that he represents one of the best chances for the X-files to be granted legitimacy and feels confident in passing the torch onto him.

Shortly thereafter, Scully goes on her maternity leave and makes it known that she has no interest in returning to the office that she’s spent nearly a decade of her life dedicated to; without Mulder present, it’s just not worth it to her anymore, and she instead returns to teaching forensics at the FBI Academy in Quantico, which was the position she held before joining the X-files. To replace her, Doggett personally recruits Agent Monica Reyes (Annabeth Gish) from the New Orleans field office, a big-time, New Age-y believer in all things supernatural and a friend of John’s from years before. Investigating this new, “super soldier”-driven alien conspiracy forms the bulk of their work.

Scully, however, finds herself inexorably drawn back to the X-files office once her son starts exhibiting extraordinary powers and Mulder is forced to go into hiding – either he or William is to be killed, the government conspiracy threatens, and Mulder decides the best option is to leave his fledgling family behind, at least temporarily. Scully, as such, serves as Doggett and Reyes’s mentor and medical expert, still performing her now-legendary autopsies on a regular basis.

1 Odds and ends

Mulder and Scully post-FBI - Complete Guide to The X-Files's Mythology

When the series ends in May 2002, a number of various storylines are left dangling, most of which are left unaddressed by 2008’s I Want to Believe, the second, standalone-story feature film.

Mulder’s return – tipped off about Mount Weather’s critical importance to the new colonist conspiracy, Mulder infiltrates the facility and discovers the set-in-stone date for colonization – news which devastates him, as it means all his hard work and sacrifices across all these long years were for nothing. Just to add insult to injury, the military arrests Mulder for his illegal entry and plans to have him be executed.

The final closing of the X-files – not content to watch their friend die, Scully, Doggett, Reyes, and Assistant Director Walter Skinner help him escape. Knowing of their role in the breakout, the FBI hierarchy disbands the X-files yet again, scattering Doggett and Reyes to the wind (Skinner is allowed to keep his position, but he pays an unknown price for his intransigence). Mulder and Scully, meanwhile, go on the lam, attempting to carve out for themselves new lives while remaining fugitives from the FBI.

A (partial) new beginning – Scully eventually lands work at a Catholic hospital in an unknown city. Several years later, the FBI tracks her there and enlists her help in getting Mulder, whom she’s been living with as a romantic couple, to temporarily return to the fold to help solve a case involving missing agents. In exchange, the Bureau agrees to quietly cease its manhunt for him, giving him some breathing room to resume his life – or what’s left of it.

CGB Spender – unable to worm his way into the new alien conspiracy, and believed dead by the wider world, anyway, the man formerly known as the Cigarette Smoking Man holes up in a series of Anasazi ruins in New Mexico, which he claims are the relics of the first shadow government in human history – in-tune with humanity’s extraterrestrial origins, the Anasazi elders somehow divine that mankind will end on December 22, 2012, and hole up in a region heavy with magnetite deposits, which will save them from the colonists’ return. Instead, the human replacements dispatch black helicopters to the area and demolish it with a series of missiles, killing Spender – and, they hope, Mulder, who was also present at the scene.

The chosen one – in keeping with their apparent foreknowledge of the impending alien colonization, various Native American cultures developed a mythology around a man who will stop the impending apocalypse, thereby becoming humanity’s savior. It is largely believed that Fox Mulder, who naturally became the perfect human-alien hybrid, is this figure of destiny, although it remains unknown whether Mulder has a part yet to play – or whether his previous actions have already fulfilled the prophecy.


Did we miss an important mythological beat? Do you have your own interpretation of the show’s previous developments – or predictions as to its new ones? Let the world know in the comments below.

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