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The Entire X-Files Mythology Timeline Explained

No series has a dense and long-running mythology quite like "The X-Files." While many shows have made their mythologies infinitely more complicated, the truth out there is "The X-Files'" follows very simple themes. All the abductions, colonization, alien viruses, and super-soldiers are byproducts of the core of the story — the relationship between Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson). These two FBI agents take on bizarre and uncategorizable cases. Eventually, they uncover something much more sinister ... something that threatens all of human existence.

For those of you interested in what this alien conspiracy is all about and who do not find Mulder's explanation from the original series finale satisfactory, this article is for you. Not only will we cover the series' entire mythology — or "mytharc" in "X-Files" fan vernacular terms — including the original series, movies, and revival series, but hopefully we'll connect all the dots in an orderly fashion and slightly enhance your appreciation for "The X-Files" as a whole. 

Grab your flashlight and tape a big "X" across your window because we're diving deep into "The X-Files" timeline.

An origin of species

In the flashback we see in 1998's "The X-Files: Fight the Future" feature film, what is now West Texas is under ice in the year 35,000 B.C. Because of the Ice Age, the aliens — later known as the Colonists — leave Earth and don't return for thousands of years. Sometime during their absence, two cavemen encounter a vicious alien creature who kills one of them and infects the other with the mysterious dark ooze later dubbed the Purity virus, aka black oil.

After this encounter and possibly others like it, human physiology begins to change. Over time, mankind evolves into its current state with much of the unused DNA (aka "junk DNA") lying dormant. The Purity stays underground for centuries, eventually mixing into black oil deposits beneath the surface and thereby earning its future nickname. After the Colonists leave Earth, they go on to colonize other planets and systems before eventually heading back to this world. 

After thousands of years, the Maya civilization predicts that an alien invasion will result in the end of the world on December 21, 2012. While this doesn't come to pass — 2012 came and went and "The X-Files" continued — the mysterious Cigarette Smoking Man (CSM) eventually implies that while the end of the world might not have happened in 2012, the year may have served as a specific extraterrestrial milestone — a new beginning, or the beginning of the end for planet Earth.

The birth of the Syndicate

In 1947 — the same year as the Roswell incident in New Mexico — the Colonists return to Earth to form an alliance with members of the United States government. These government officials, known later as the Syndicate, start the Project to prepare the Earth for the Colonists' arrival. To this end, the Syndicate and the Colonists begin human cloning experiments that eventually lead to their super-soldier program.

Less than three decades later in 1973, the Syndicate learn of the Colonists' ultimate plans to annihilate the entire human race by infecting humans with the black oil. Recognizing the aliens' superior technology, the Syndicate help the Colonists disseminate the black oil virus across the globe while experimenting with the creation of alien-human hybrids. Unbeknownst to the Colonists, the hybrids are immune to the virus. Bill Mulder, a member of the original Project, disagrees with the Syndicate and Colonists' plans and begins working on a vaccine to save humanity from the Purity.

Unfortunately, part of the Syndicate's agreement with the Colonists involves giving up a member of their own families for the aliens' experiments. C.G.B. Spender, aka the CSM, gives up his ex-wife Cassandra. Bill Mulder very reluctantly chooses his son, Fox. But since the Colonists' need a young girl, they take his daughter Samantha instead. In return, the Colonists provide the Syndicate with an alien fetus for experimentation.

The opening of the X-Files

In one of the very first X-Files, Special Agent Arthur Dales (played as an old man by Darren McGavin, "Kolchak the Night Stalker" himself) works with Bill Mulder on a case involving an alien parasite. The experience prompts Dales to continue the hunt for all things strange and paranormal for decades before eventually retiring. The FBI remains free of agents preoccupied with spooky cases until Bill Mulder's son grows up, pursues a career in law enforcement, and joins the FBI.

Fox Mulder uses his connections in the Senate and the State Department to get himself transferred to the X-Files unit. Traumatized from witnessing his sister's abduction as a child, Mulder uses every resource he has to find answers about what happened to Samantha and connect the dots between little green men in UFOs and the United States government. He makes a few friends and plenty of enemies along the way. Mulder's original partner and love interest Diana Fowley works with him for years before eventually leaving to secretly join the Syndicate.

Around this time, Syndicate member Ronald Pakula — most commonly known by his codename "Deep Throat," an alias he shares with the Watergate informant — unofficially defects from the group and begins feeding Mulder information on the alien conspiracy, hoping to expose the truth.

Mulder gets a new partner

In 1993, the CSM handpicks Dana Scully as Mulder's new partner on the X-Files. The Syndicate elder hopes that Scully's scientific mind, medical background, and general skepticism towards the supernatural will discourage Mulder's investigations into Syndicate affairs. What the CSM doesn't count on is all the logic-defying phenomena Scully will see during her time with the X-Files. He also fails to anticipate the bond of friendship and love that grows between her and Mulder.

During this first year together, Mulder and Scully investigate many strange cases. Some of the mysteries indirectly connect back to the Colonists, such as the cases involving alien signals, metallic implants, abduction, and even UFOs, like the one Mulder catches a glimpse of shortly before his memory of the sight is erased. Other times, the agents battle mutants, parasites, and other paranormal creatures that fall under the "unexplained" category. All these experiences bond the agents together and only solidify Mulder's search for the truth.

In the Season 1 finale, Mulder discovers the alien-human hybrid program. This knowledge puts him in grave danger with the Syndicate who send men in black to abduct him. Fearing for Mulder's life, Deep Throat works with Scully to steal the frozen alien fetus and uses it as leverage to get Mulder back in one piece. Amid all the chaos, the CSM has Deep Throat killed for his part in exposing the project and arranges to close the X-Files.

Scully's abduction

Of course, the X-Files don't remain closed. After all, the Fox Network would never do something as short-sighted as cancelling one of their all-time most popular shows, especially after only one season...  

Anyway, Assistant Director Walter Skinner – Mulder and Scully's longtime ally and occasional foil — quickly puts them back on the strange and paranormal beat, believing it's what the Syndicate fears most. Due to Deep Throat's death, a new informant known only as X — a reference to the similarly named character in director Oliver Stone's 1991 film "JFK" — begins feeding Mulder information about the conspiracy.

Before the X-Files officially reopens, Scully is kidnapped by a former FBI agent and abductee named Duane Barry who believes that he can stop the Colonists from repeatedly abducting him if he hands them Scully in his place. But Scully isn't abducted by the aliens; The Syndicate experiment on her and place an implant at the base of her neck. This abduction marks the beginning of Scully's series-long arc that entails her getting cancer and encountering all kinds of fertility-related issues connected to this ordeal.

A few episodes later, Scully resurfaces in a coma and no one understands why she won't wake up. In a rage, Mulder confronts the CSM after Skinner points Mulder in the right direction. The CSM tells Mulder that he likes him and Scully, which is why Scully is back. Eventually, Scully wakes from her coma with no memory of her abduction or the events in between, and she finds Mulder's presence in the hospital very comforting.

The conspiracy strikes back

Eventually, the Colonists catch on to the Syndicate's double-cross attempt to save themselves from the black oil. To resolve this issue, the Colonists send a virtually unkillable shape-shifter, casually referred to as an Alien Bounty Hunter, to Earth to wipe out the Syndicate's various batches of clones, including the sets known as the Gregor and Samantha series, the latter being clones of Mulder's sister.

Soon after, the Department of Defense is hacked and the files are leaked to Mulder and Scully. Since they are coded in Navajo, Scully asks Albert Hosteen to translate them onto a tape that becomes the only physical proof of the alien conspiracy. The Syndicate attempt to track down the tape and dispatch their toady Alex Krycek to kill Bill Mulder, who nearly confesses everything about the Project to his son.

On good intel, Mulder and Scully travel to a mining facility that the group uses to store their own abduction records, including a recently updated file on Scully. It's here that Mulder learns he was originally meant to be abducted, rather than Samantha. Following their escape, the agents and Skinner make a deal with the CSM, using a threat of exposure as leverage so that they can return to their normal lives without being hunted by the group's secret police, the Men in Black.

Abduction sickness and alien autopsies

After Scully discovers and removes a metallic implant from the back of her neck, the Syndicate are alerted to her progress. In response, Krycek attempts to kill her just as he did Bill Mulder, though he accidentally kills Scully's sister Melissa instead. Soon after, Mulder discovers a Japanese alien autopsy video and Scully recognizes one of the men in the video from her own abduction. 

While investigating a group of abductees, Scully learns that the group of women all have similar abduction stories and metallic implants reminiscent of her experience, and they're all dying of cancer. It's a bit eerie and entirely heartbreaking. Later, we find out that their cancer is a built-in failsafe the that the Syndicate include in their metallic implants to keep their test subjects from removing them, which is something that comes back to haunt Scully later on.

The alien autopsy video ultimately leads Mulder to a secret railway where he believes an alien-human hybrid is being transferred across the country by train. However, the Syndicate observe Mulder's progress in uncovering their secrets. In order to get rid of Mulder and keep their operation out of the Japanese government's knowledge, they blow up the train. X saves Mulder's life at the last moment, but Mulder is left with no evidence or direction.

The Project presses on

After uncovering a sunken vessel filled with the alien black oil, Alex Krycek reappears possessed by the parasitic alien virus. During this time, Mulder attempts to retrieve the conspiracy tape from Krycek, who had previosuly stolen it from Skinner. Krycek plays hard to get and gives it to the CSM in exchange for the location of a missing UFO. The alien-possessed Krycek finds the UFO in North Dakota and the alien virus makes contact with the spacecraft. Concurrently, Skinner is almost killed by a man in black who assisted Krycek with the murder of Melissa Scully, though Skinner recovers.

Months later, after Mulder and Scully discover a man named Jeremiah Smith who has the ability to heal any wound, they learn that Smith is a part of the Syndicate's greater project and that there are other Jeremiah Smiths all across the country. After being pursued by an Alien Bounty Hunter, one of the Smiths takes Mulder to a Canadian farm populated by young clones of his sister Samantha. These clones are bred to harvest the smallpox-carrying bees the Colonists plan to use for spreading the Purity pathogen.

Simultaneously, the Syndicate believe that they have a leak. After some strategic planting of false information, they assassinate X. In his final moments, X tips Mulder off to finding Marita Covarrubias, a high-ranking Syndicate employee who becomes another ally in his quest for the truth.

To Russia without love

Alex Krycek doesn't stay down for long. He quickly recovers from his possession and seeks out Mulder and Scully after turning on the CSM and promising to expose the "Cancer Man" to the world. After Krycek leads the agents to a meteorite with fossilized alien bacteria attached, Mulder turns to Marita Covarrubias for help. She points Mulder to Russia, the source of the rock, though he's unfortunately forced to take Krycek with him since Krycek speaks fluent Russian and Mulder doesn't.

Predictably, Krycek double-crosses Mulder and hands him over to the Russian black oil vaccination trials. Mulder is infected with the black oil, but the Russian vaccine prevents the alien pathogen from taking over his body. The effects of the dormant virus come back to haunt Mulder in different ways later, but at this point he's apparently free of any alien influence. Krycek, hoping for revenge against the CSM, sends a KGB assassin to kill the Syndicate's scientists working on their own black oil vaccine.

Not everything works out well for Krycek here. Hoping to save him from the black oil vaccine trials, a group of Russian test subjects overpower Krycek and saw off his left arm. Krycek survives the ordeal, but it slows him down for a while.

Cancer cured and faith lost

After encountering a cancer-eating mutant, Scully discovers that she has developed a rapidly progressing form of brain cancer that should soon prove lethal, just like the other abductees who removed their implants. Mulder — with help from his conspiracy theory sidekicks the Lone Gunmen — breaks into a highly secure research facility and retrieves Scully's missing ova. Eventually, Scully's condition causes their ally Walter Skinner to make a deal with the CSM to cure her, but nothing comes of it other than Skinner being manipulated into covering up some Syndicate-related deaths.

With no other options, Mulder goes to the CSM for help. The CSM reveals that putting a new implant into Scully's neck would stop the cancer completely. Mulder convinces Scully to agree to this, and her cancer does indeed go into remission. But as Mulder searches for answers, he is confronted with an alternate conspiracy theory. He begins to believe that aliens are a fictitious smoke screen for the military-industrial complex that rules the nation and the world from the shadows. This leaves Mulder broken and disheartened, losing his faith in his mission. Ironically, Scully's episode with cancer renews her Catholic faith, making her slightly more open to supernatural possibility.

Around this time, the agents also learn that the government used Scully's ova to genetically engineer a young girl named Emily who, as it turns out, Scully gave birth to during her abduction. Emily is raised elsewhere until she dies. Her body, the only evidence of her existence, mysteriously disappears.

A rebel alliance

As it turns out, Mulder isn't the only person opposed to the impending alien invasion. A particular group of Colonists called the Alien Rebels — known for their grotesque appearance due to having sealed every orifice shut to protect themselves from the Purity — begin destroying the Colonists' work on Earth. As this continues, Mulder and Scully befriend the CSM's ex-wife Cassandra Spender, who claims to have been abducted multiple times and is the first alien-human hybrid created without cloning. Mulder doesn't believe her at the time, but he comes around.

The Rebels begin killing abductees, hoping to destroy the Colonists' work and stall colonization. But when the Rebels attempt to take out Cassandra, the Colonists strike back, taking her with them after killing roughly a dozen defectors from their cause. Presented with too much evidence to remain cynical, Mulder regains his faith and returns to the fight to expose the truth.

Months later, the agents encounter a young boy named Gibson Praise, whose active junk DNA allows him to read minds. This makes him a target for the Syndicate, who wish to take his special brain for their own purposes. Mulder and Scully unsuccessfully try to protect the boy, and he's taken to be experimented on by the Syndicate. In all the commotion, the CSM steals Samantha Mulder's file and burns the X-Files office down, closing the X-Files once more.

Fighting the future

Immediately after these events and between the show's fifth and sixth seasons, the very first "X-Files" movie, often subtitled "Fight the Future," takes place. In "Fight the Future," the agents pursue the origins of four dead bodies found in the ruins of a bombed building in Texas. These four people had apparently been killed before the bombing. As it turns out, they had been infected by the black oil, which is using its hosts to birth a new species of more aggressive alien lifeforms, sort of like in the "Alien" movie franchise.

As the agents travel the globe, Mulder and Scully discover a Syndicate facility in Texas cultivating the virus-spreading bees. Unfortunately, one of the bees catches a ride home with them to D.C. where it stings and infects Scully. And it gets worse; Scully is abducted again. With the help of Skinner and the Lone Gunmen, Mulder escapes Syndicate-affiliated pursuers only to run into a sympathetic Syndicate leader who has decided to switch sides. This Well-Manicured Man gives Mulder the Syndicate's vaccine against the black oil as well as Scully's location in the Antarctic.

After Mulder rescues Scully, they're chased by aliens on their way out of the icy facility. Sadly, a very dazed-and-confused Scully fails to witness the facility rising up and flying away, revealing itself to be a UFO. Afterward, the X-Files officially reopen.

The Syndicate is destroyed

Although the X-Files are open for business, Mulder and Scully aren't initially reassigned to them. As it turns out, Special Agents Jeffrey Spender and Diana Fowley head the unit for a while. During this time, the Syndicate are infiltrated by Alien Rebels and the FBI is infiltrated by the Syndicate. Alex Krycek, once again working on behalf of the Syndicate, blackmails Skinner. But this status quo doesn't last long. When Cassandra Spender returns from her most recent abduction, she explains to Mulder and Scully that the Colonists aren't the friendly green men she once thought they were. Instead, they intend to wipe out humanity.

Cassandra reveals that the Alien Rebels plan to annihilate the black oil virus entirely — a plan that began a year prior during their campaign of killing abductees. The Rebels strategically orchestrate an attack on the Syndicate and their families that entails gathering them together and burning them alive. This puts an end to the entire Syndicate except for the CSM and Diana Fowley, who escape the ordeal and make it out safely. Cassandra herself, who has been taken by the Syndicate to be offered up to the Colonists, is also killed by the Rebels. It's a pretty horrific scene.

As Agent Spender's father, the CSM attempts to conscript his son into working with him, but Spender sides with Mulder, Scully, and Skinner to try to stop Cassandra Spender's death. Agent Spender recommends that Mulder and Scully be reinstated to the X-Files, which prompts the CSM to shoot his traitorous son.

New revelations

After an alien spacecraft is discovered off the coast of Africa, Mulder begins to experience strange symptoms after touching a metallic piece of it. As it turns out, the alien shard reactivates the dormant black oil virus that Mulder was infected with in Russia. To investigate the ship, Scully travels to Côte d'Ivoire and discovers that the craft contains passages from various holy books, including the Bible, and a prehistoric map of the human genome which invites countless questions about the origins of life.

While Scully is away, the CSM kidnaps Mulder, believing the agent to have become an alien-human hybrid. This is where the CSM reveals himself as Mulder's biological father and admits that by implanting Mulder's genetic makeup into himself, he might survive the coming colonization. Eventually, Scully returns to save Mulder, only to have to break the news that the CSM killed Diana Fowley shortly after she helped Scully's rescue efforts.

Months later, after his recovery, Mulder finally learns the truth about Samantha. After years of meeting clones of his sister, he learns that she was returned by the Colonists in the 1970s and lived a life with her biological father and half-brother — the CSM and Jeffrey Spender. Eventually Samantha died, becoming a spirit known as a "walk-in," which allows Mulder to reunite with her, albeit briefly. Afterward, he and Scully return home, his life-long mission is finally complete.

Super-soldiers and a new conspiracy

Seven years after their first case there, the agents are called back to Oregon by Billy Miles, a boy and abductee they helped during their prior visit. In a desperate attempt to restart the Project, the CSM hopes to retrieve a UFO from the Oregon town. Mulder and Scully hope to find it first. In Season 7's final moments, Mulder is abducted along with a host of other people; Scully learns that she's pregnant, and Alex Krycek and Marita Covarrubias finally kill the CSM ... or so it appears. 

But even without the CSM, the Colonists continue their plot, using their Alien Bounty Hunters to create new human-alien replacements known as super-soldiers. As Scully and Skinner search for Mulder with help from new X-Files assignee Special Agent John Doggett, what appears to be Mulder's corpse returns to Earth. After months, Mulder is resurrected as his body begins the alien replacement process triggered by his previous exposure to the black oil virus. Thankfully, Scully finds a way to save him and prevent his transformation into a super-solider.

Billy Miles, on the other hand, becomes a super-soldier and begins erasing all evidence of the Project, making sure the Colonists' mission remains a secret. Mulder, Scully, Doggett, Skinner, and newcomer Monica Reyes fight back to expose the conspiracy, killing Krycek in the process. As Scully gives birth to her son, multiple super-soldiers gather to watch in awe, believing the child to be something more...

William and the truth out there

Soon after the birth of Mulder and Scully's son, William, Mulder goes into hiding, hoping to keep his family safe from the conspiracy he continues to unravel. As Scully, Doggett, and Reyes continue the X-Files, it's revealed that William is a telekinetic alien-human hybrid, making him a target for different factions of super-soldiers, alien cultists, and the Colonists themselves. Doggett and Reyes work plenty of strange X-Files, although their dynamic doesn't quite equal that of Mulder and Scully.

As Season 9 progresses, Scully continues to fight for her son's safety and search for Mulder. In the process, William's alien DNA is temporarily set on "standby mode" after Jeffrey Spender returns with an antidote. Spender reveals that the Colonists need William for a successful invasion. Because of this, Scully ultimately gives him up for adoption. William is renamed Jackson Van De Kamp by his new parents.

In the original series finale, Mulder is tried for the murder of a Marine named Knowle Rohrer, who's actually an unkillable super-soldier. Scully, Skinner, Doggett, Reyes, and Gibson Praise — who has been hiding Mulder for the past year — all testify in Mulder's defense, but it's no use. Mulder and Scully are forced to flee from the military, only to learn from the CSM, who somehow turns up alive, that colonization is set for December 21, 2012. Men in Black apparently kill the CSM and Mulder and Scully leave the FBI.

The conspiracy lives on

After being pardoned for their alleged crimes, Mulder and Scully return to the X-Files. With the date of colonization having come and gone — apparently due to climate change keeping the Colonists from invading the Earth — the Colonists and super-soldiers have mysteriously disappeared. Meanwhile, the CSM has somehow escaped getting his face blown off by Men in Black and now searches for Mulder and Scully's son William, currently known as Jackson, who he now claims to have fathered himself via genetic experimentation on Scully during one of her abductions. Yikes.

Having co-opted both Monica Reyes and Walter Skinner into working for him before he gets them both brutally murdered, the CSM's latest goal revolves around igniting the alien Spartan virus to decrease the global population. Throughout the revival series, the CSM is also in direct conflict with two surviving members of the Syndicate, but they don't last terribly long. For five out of the 16 total revival "X-Files" episodes, Mulder and Scully search for their long-lost son. The other 11 episodes are centered around various paranormal cases.

Eventually William is found, but the reunion is short lived after the CSM seemingly kills him. In a rage, Mulder shoots the CSM multiple times, and the villain's body washes away in the river. As Mulder and Scully mourn William, Scully reveals that they're pregnant with another miracle child. Elsewhere, William — having survived due to his alien abilities — escapes, leaving him free to live his own life far away from alien conspiracies and the secret government agencies and all the other "X-Files"-related insanity.