Mythology

Pilot

1x01
Introduces FBI agents Fox Mulder and Dana Scully.
Mulder is a believer in the paranormal due to his sister Samantha's abduction, which he believes was by aliens.
Scully is assigned to debunk Mulder's work on the X-Files.
Evidence of alien abductions and implants found in the first case.

Deep Throat

1x02
Mulder and Scully investigate a case involving missing pilots and possible government experiments with UFO technology.
Deep Throat provides information suggesting the military is conducting secret tests using alien technology.
Introduces the concept of the government covering up extraterrestrial encounters.

Fallen Angel

1x10
Mulder investigates a UFO crash site in Wisconsin, covered up by the government.
Introduction of Max Fenig, a UFO enthusiast who is abducted by aliens.
The government retrieves the UFO wreckage, further cementing the conspiracy.

Eve

1x11
Although not directly related to aliens, this episode touches on government experiments, specifically genetic cloning, hinting at larger conspiracies.

E.B.E.

1x17
Mulder and Scully investigate a truck supposedly carrying an E.B.E., leading to more revelations about government cover-ups.
Introduction of "The Lone Gunmen," a trio of conspiracy theorists who assist Mulder.
Deep Throat admits to the existence of aliens and that the government is hiding them.

The Erlenmeyer Flask

1x24
Mulder and Scully discover evidence of a government project involving human-alien hybrids.
Deep Throat is killed by government agents after revealing too much.
The episode ends with Scully seeing a preserved alien fetus, confirming the existence of extraterrestrial life.

Little Green Men

2x01
Mulder and Scully continue to investigate despite the closure of the X-Files division.
Mulder experiences a close encounter at an abandoned SETI facility, but the evidence is destroyed.
Introduction of Senator Richard Matheson, a government insider helping Mulder.

Sleepless

2x04
Introduction of Alex Krycek, an FBI agent secretly working for the conspirators.

Duane Barry

2x05
Duane Barry, a former FBI agent and alien abductee, kidnaps Scully, believing she will be abducted instead of him.
Introduction of the alien abduction phenomenon as a recurring theme.

Ascension

2x06
Scully is abducted by either aliens or government agents working with them.
Mulder desperately tries to rescue her, encountering the government's resistance.

Colony

2x16
Introduction of the Alien Bounty Hunter, who is tasked with eliminating alien-human hybrids.
Mulder encounters clones of his sister Samantha, suggesting her abduction was part of a larger experiment.

End Game

2x17
Mulder learns more about the alien colonization plan, where aliens are creating hybrids.
The Alien Bounty Hunter kills one of the Samantha clones.
Mulder is almost killed but saved by the Syndicate, who are involved in the alien conspiracy.

Anasazi

2x25
Kenneth Soona, aka The Thinker, is a hacker known by The Lone Gunmen. He hacked into the DOJ infrastructure and stole confidential digital documents.
Mulder receives a digital tape containing the government's most secret files on extraterrestrials.
Mulder discovers his father was involved in the conspiracy and that Samantha's abduction was part of it.
Mulder's father is killed by Krycek, and Mulder, with the help of Scully, is left to decode the files, which point to human-alien hybrid experiments.

The Blessing Way

3x01
Mulder is saved by a Navajo shaman after nearly being killed.
Scully is pursued by the Syndicate as she tries to decrypt the digital tape.
Introduction of the Well-Manicured Man, a higher-up in the Syndicate, who hints at the existence of a larger plan.

Paper Clip

3x02
The digital tape is taken from Skinner by Krycek and two other men, apparently working for the Smoking Man. But the CSM orders to kill Krycek. He nearly escapes and now threatens Smoking Man, being the only one to have the tape...
In exchange for Mulder and Scully's safety, Skinner asks Albert Hosteen to share the content of the digital tape with twenty other men. Therefore, if CSM tries to harm Mulder or Scully, Albert or his men will share the content of the tape... except that we don't know if Skinner is bluffing or not.
After World War II, the US government provided asylum to Nazi criminals in exchange for their scientific knowledge. This operation was known as operation "Paper Clip". Viktor Klemper was one of them and can be seen on a picture in front of the Strughold Mining Company in West Virginia in 1973 (or 1972) along with Smoking Man, Well Manicured Man and Bill Mulder.
Inside the Strughold Mines, Mulder and Scully discover "lots and lots" of medical files. They all contain a birth certificate, a small pox vaccination certificate and a tissue collection.
There are files about Scully and Samantha Mulder, although it seems that originally it was Fox Mulder who should have been in the file.
WMM explains that in 1947, a spacecraft crashed in New Mexico. A body was recovered from the ship. This incident coincided with the end of WWII and the paper clip operation. Dr. Mengele wanted to create a race of supersoldiers. Klemper apparently worked with him. Viktor Klemper tried to create an alien human hybrid. The aliens that Mulder saw in 'Anasazi' were test subjects.
When Bill Mulder realized what the medical data was being used for, he objected strenuously. With the threat of nuclear holocaust, the government instructed men like Bill Mulder to gather genetic data on the general population for the purposes of post-apocalyptic identification. They did it through the small pox vaccination, collecting data on hundreds of millions of Americans. So Klemper had access to a DNA database of nearly everyone who was born since 1950.
They took Samantha Mulder as insurance because Bill Mulder threatened to expose the project. Bill asked his wife to choose which child would be taken away, but she couldn't do it. So Bill has chosen his daughter.

Nisei

3x09
Since the end of WWII, Japanese doctors did some experiments on test subjects, in order to create a possible alien-human hybrid. Dr Shiro Zama (aka Takeo Ishimaru) is one of them. He was the commander of an elite section of the Japanese medical corps known as 731. A unit known to have experimented on humans. They performed vivisections without anaesthesia, tested frostbite tolerance levels on infants, exposed innocent prisoners of war to diseases, the plague. Like their Nazi counterparts, they were never brought to justice. They were on US soil continuing the work the Nazis were doing, trying to create an alien-human hybrid.
They also were conducting tests on humans, like Scully, who recognizes Shiro Zama.
Scully discovers women also abducted and learns that they are all going to die from an unknown type of cancer.

731

3x10
Dr. Ishimaru worked on leper, but his real work was to do tests on homeless, on the insane. They were brought here and subjected to diseases and radiation tests.
Dr. Ishimaru (aka Shiro Zama) began to conduct his work in secret, not sharing with those with those who'd risked much in giving him his asylum. That is why, now that he created the ultimate weapon as a alien-human hybrid, the syndicate take care of the situation and delete every proof (kill test subjects, kill Dr. Ishimaru, etc.)
Scully had been brought in one of those train cars and Ishimaru did put the implant into her neck.
Zama maybe create a person capable of surviving any radiation. Shiro wanted to take the man with him in Japan, but the US government didn't wanted to share. Zama succeeded where the others failed. Maybe he is an alien-human hybrid.
Mulder boards a train carrying an alien-human hybrid and uncovers more about the government's experiments.
Scully learns that the smallpox vaccine was used to catalog people for potential abductions and hybrid experiments.

Piper Maru

3x15
Introduction of the black oil, a sentient alien virus that possesses humans.
Mulder and Scully investigate a French salvage ship that brings the black oil back from a downed UFO.
Krycek is selling informations from the digital tape of "Anasazi". That's how the French government found out about the location of a UFO inside the Pacific Ocean. But they find black oil instead of the UFO, which was already pulled out by the Talapus boat ("Nisei").

Apocrypha

3x16
It was really a UFO that Mulder "saw" in "Nisei". From there, the black oil goes into three people (including Krycek) in order to go back inside the UFO. The UFO was shot down during WWII.
The black oil is revealed to be a means of alien colonization, with the ability to control humans.
The Syndicate is shown to be working with the aliens, facilitating the colonization in exchange for their own survival.

Talitha Cumi

3x24
Introduction of Jeremiah Smith, a healer with alien abilities, who can shapeshift and heal others. Smith's abilities suggest a connection to the alien colonization project.
We learn in this episode that the Smoking Man and Mulder's mother had an affair. CSM: "I remember water-skiing down there with Bill. He was a good water-skier, your husband. Not as good as I was, but then... that could be said about so many things."
The Smoking Man is asking Mulder's mother if she remembers where is the same weapon as the one used by the Alien Bounty Hunter in "Colony".
He wants this weapon in order to kill Jeremiah Smith, an alien who no longer believe in The Project. He uses his healing powers on population, that's the reason why the CSM wants to kill him.
But the CSM never kills Jeremiah Smith. Smith tells the CSM that he has lung cancer, so he heals him and get free again.
The date of the colonisation is set.

Herrenvolk

4x01
Jeremiah Smith takes Mulder to see a place where there is a special flowering shrub. It is being grown for pollen by a colony of alien-human hybrids.
Mulder sees clones of his sister Samantha. The children are stationed here and are part of an agrarian workforce. These clones are serial ovotypes.
Clones of Jeremiah Smith worked at the social security agency. They collected data. The lists starts by SEP, meaning Smallpox Eradication Program. In fact, Scully gets a microscope picture from one of the inoculants used in the smallpox vaccine. She thinks that this protein is a tag, some kind of a genetic mark that she got when she was inoculated against smallpox as a child, like every American during the last 50 years. This master plan is as followed: the US population is catalogued, tagged and inventoried.
The Alien Bounty Hunter kills the clones to keep the project secret.
X is killed because the Syndicate discovered that he was Mulder's informant. But just before he dies, he gives Mulder a clue about how to find a new informant in the United Nations. Her name is Marita Covarrubias.
Finally, CSM asks the Alien Bounty Hunter to heal Mrs Mulder.

Musings of a Cigarette Smoking Man

4x07
This episode provides background on the Cigarette Smoking Man, revealing his deep involvement in the government's conspiracies, including the Kennedy assassination and UFO cover-ups.
Though not a direct continuation, it offers critical insights into the motivations behind the main antagonist.

Tunguska

4x08
Mulder and Krycek travel to Russia to investigate the black oil, discovering its use in experiments on Russian prisoners.
Mulder: "June 30, 1908. Tunguska tribesmen look into Siberian sky and see a fireball streaking to Earth. When it hit the atmosphere, it created a series of cataclysmic explosions, considered to be the largest single cosmic event in the history of civilisation - 2,000 times the force of the bomb that was dropped on Hiroshima."
Krycek: What was it?
Mulder: It's been speculated that it was a piece of a comet or an asteroid or a piece of antimatter. The power of the blast levelled trees in a radial pattern for 2,000 kilometers. No real evidence has ever been found to provide a satisfying explanation for what it was.
In Tunguska, men are doing experiments on Russian prisoners in a gulag. They are exposed to the black oil, a virus that was found inside Tunguska's rocks. Those rocks apparently come from a comet fallen from the sky, coming from Mars.
The black oil is confirmed to be a key component of the alien colonization strategy.

Terma

4x09
Mulder learns that the Russians are working on a vaccine against the black oil, which could be used to resist the alien colonization.
The Russians know that the US Syndicate is working on their own inoculation with the black oil. So they try to do everything to stop the US to conduct further experiments.
The Syndicate's global connections and their collaboration with various governments are further explored.

Memento Mori

4x14
Scully learns that she has a brain tumour, believed to be a result of her abduction and experimentation by the Syndicate. Along with Mulder, they investigate women from "Piper Maru" that were abducted by the government. Out of twelve women, eleven are dead.
Mulder discovers that Scully's ova have been taken from her during her abduction. "Harvest during her abduction through a radiation procedure that caused superovulation."
Mulder: "Why?"
- "For fertilisation. They constitute one half of the necessary raw materials."
Mulder : "For genetic hybridisation. For reproduction. These women are your birth mothers."
- "Barren now... from the same procedure that caused their cancer. And now they're left to die, their condition hastened by the men running this project."

Tempus Fugit

4x17
Mulder and Scully investigate the crash of a commercial airliner, which they believe was caused by a UFO.
They uncover evidence of alien involvement and government attempts to cover it up.

Gethsemane

4x24
Mulder is shown what appears to be an alien body, suggesting the government has finally been caught in its lies.
Scully is skeptical and discovers that the body is a hoax, part of a disinformation campaign by the Syndicate to discredit Mulder.

Redux

5x01
Mulder infiltrates the Department of Defense to find a cure for Scully's cancer, believing it to be related to the government's experiments.
The Cigarette Smoking Man offers Mulder the cure, revealing that he may know more about Mulder's sister.
The Syndicate's disinformation campaigns are highlighted, and Mulder becomes increasingly disillusioned.

Redux II

5x02
Scully is miraculously cured of her cancer after Mulder retrieves the cure.
The Cigarette Smoking Man is shot, but his survival and escape suggest his deep connections and the Syndicate's power.
Mulder discovers more evidence pointing to the Syndicate's involvement in a massive conspiracy but is unable to act on it.

Patient X

5x13
Mulder meets Cassandra Spender, a woman claiming to be a multiple alien abductee.
In Russia, Krycek steals a vaccine against the black oil (developed by the Russians).
Well Manicured Man: "In the final phases before it begins, there will most likely be assemblies." This so-called "final phase" will take place in 15 years.
There is an act of war against the Syndicate's plans by alien rebels. One of them mutilated himself in order not to fear the black cancer. This man is "a resistance fighter against the alien colonists".
Well Manicured Man wants deeply to either fight the colonists with the help of the vaccine, or side with the resistance, but the other members of the Syndicate still want to cooperate with the colonists.
Introduction of Cassandra Spender, a multiple abductee who believes she is a part of the alien colonization plan.
Mulder begins to question the existence of aliens, considering the possibility that everything is a government hoax.

The Red and the Black

5x14
Krycek: "There is a war raging, (...) you and I and five billion other people are gonna go the way of the dinosaur. I'm talking planned invasion. The colonisation of this planet by an extraterrestrial race. Kazakhstan, Skyland Mountain, the site in pennsylvania, they're all alien lighthouses where the colonisation will begin, but where now a battle's being raged. A struggle for heaven and earth, where there is one law: fight or die. And one rule: resist or serve." Krycek again: "The mass incinerations were strikes by an alien rebellion to upset plans for occupation."
The conflict between two alien races is introduced: the Colonists and the Rebel aliens who resist colonization.
Cassandra Spender is revealed to be the key to the alien colonization plan, as she might be the first successful alien-human hybrid.
Mulder learns more about the Syndicate's involvement in facilitating the colonization.

The End

5x20
Mulder and Scully discover a little boy named Gibson Praise. He's got psychic abilities far from everything Mulder has ever seen. He can read inside people's mind.
Chessplayer's murderer: "The kid is a missing link."
Mulder: "To what? (pause) He's genetic proof, isn't he?"
The Syndicate's plans begin to unravel as internal tensions rise.
The X-Files office is burned down, destroying much of Mulder and Scully's evidence.
Introduction of Jeffrey Spender, Cassandra's son, who becomes involved in the conspiracy against his will.

The Beginning

6x01
FBI woman: "The plot is for these spacelings to take over the planet, aided by a group of men here on Earth..."
Mulder: "A shadow conspiracy within our own government."
FBI woman: "... who are growing corn in the middle of the desert, which features pollen, which was genetically altered to hold a virus, which will be taken away by bees whose sting transmits the virus, causing the growth of an extraterrestrial biological entity inside the human host?"
The company is called Roush. We learned about Roush in "Redux".
Mulder and Scully are reinstated to the X-Files but under greater scrutiny.
The alien virus, black oil, begins to show its true potential as a means of alien reproduction.
The Syndicate's plans become more urgent as colonization draws nearer.

Two Fathers

6x11
Smoking Man: "We had a perfect conspiracy... with an alien race. Aliens who were coming to reclaim this planet and to destroy all human life. Our job was to... secretly prepare the way for their invasion. To create for them a slave race of human/alien hybrids."
This plan was "kept secret for over 50 years, ever since the crash at Roswell." Those plans would have worked, but "a rebel alien race came to destroy them."
The Syndicate's origins are revealed, including their pact with the alien Colonists to facilitate colonization in exchange for survival.
Cassandra Spender is revealed to be the first successful alien-human hybrid, making her crucial to the colonization plan.
Jeffrey Spender is manipulated by the Syndicate and his father, the Cigarette Smoking Man, to keep the truth from Mulder.

One Son

6x12
In November 1973, every member of the Syndicate had to give away a member of his family to the aliens.
Bill Mulder wanted to use the alien DNA given by the aliens to make a vaccine.
The Syndicate/alien plan was the members of the Syndicate to be transported by the colonists and be prepared to receive the hybrid genes.
The Syndicate is exterminated by the Rebel aliens, who burn them alive to stop the colonization.
The Cigarette Smoking Man's full betrayal and manipulation of everyone around him are revealed.
Mulder learns that the Rebel aliens are trying to stop the colonization, but at great cost.
The Syndicate's role in the conspiracy ends, but the alien threat remains.

Biogenesis

6x22
Mulder and Scully discover evidence suggesting that human life on Earth was seeded by aliens.
A mysterious artifact found in Africa contains what appears to be the key to unlocking human DNA's extraterrestrial origins.
Mulder begins to experience severe neurological symptoms linked to the artifact, suggesting a deeper connection to the aliens.

The Sixth Extinction

7x01
Scully continues her investigation in Africa, discovering more about the ancient alien artifact and its connection to human evolution.
Mulder's condition worsens, and it becomes clear that his mind is being overwhelmed by knowledge from the artifact.
The artifact suggests that the aliens were responsible for the development of human consciousness.

The Sixth Extinction II: Amor Fati

7x02
Kritschgau: "Two years ago your partner was infected with a virus he claimed was alien. A virus reactivated in him by exposure to a source of energy also alien."
Smoking Man (talking about Mulder): "He's immune to the coming viral apocalypse."
Smoking Man asks doctors to perform a medical procedure on him and Mulder. He orders them to give him Mulder's powers.
Mulder experiences visions of an alternate life, where the alien colonization has already occurred, and he lives in a false sense of peace.
The Cigarette Smoking Man attempts to manipulate Mulder into joining the alien colonization effort. Mulder ultimately rejects this vision, reaffirming his commitment to stopping the alien threat.

Sein und Zeit

7x10
Teena Mulder (Mulder's mother) dies in this episode. She was very ill and finally killed herself.

Closure

7x11
After her abduction, Mulder's sister lived with Jeffrey Spender in April Basecamp. For years, she was a test subject. She died a few years after her abduction, becoming a "walk-in", a soul made of starlight.

Requiem

7x22
Mulder and Scully return to the site of their first X-Files case, where an alien ship is preparing for colonization.
The alien ship abducts Mulder, marking a significant shift in the series.
Scully discovers she is pregnant, raising questions about the nature of her pregnancy and the involvement of the aliens.

Within

8x01
Agent John Doggett is assigned to find Mulder, who has been abducted.
Scully continues to investigate the alien conspiracy while dealing with her pregnancy.
Mulder's abduction is tied to the ongoing alien colonization plans.

Without

8x02
The Alien Bounty Hunter returns, searching for Mulder and those connected to him.
Scully's pregnancy becomes increasingly mysterious, with implications that it may be connected to the alien experiments.

Per Manum

8x13
Flashbacks reveal that Scully may have been subjected to alien fertility experiments, raising doubts about the origins of her pregnancy.
The possibility that Mulder is the father is suggested, but the alien involvement is not ruled out.

This Is Not Happening

8x14
Jeremiah Smith is healing multiple abductees.
Mulder is found, but he is in a severely weakened state, having been subjected to further alien experimentation.
The return of abductees in a similar condition suggests the aliens are continuing their work on human-alien hybrids.

Deadalive

8x15
Alex Krycek wants Skinner to kill Scully's baby.
Mulder is revived from near-death, but the process raises further questions about the alien involvement in his condition.
The episode delves into the possibility of alien resurrection technology and its implications for the colonization plan.

Essence

8x20
Scully's pregnancy reaches its climax as she prepares to give birth.
The alien Super Soldiers, a new breed of human-alien hybrids, are introduced as the next phase in the colonization plan.
Mulder and Doggett uncover more about the Super Soldiers' role in the impending colonization.

Existence

8x21
Scully gives birth to her son, William, who is revealed to have alien-related powers.
The Super Soldiers see William as key to their plans, but Mulder and Scully manage to protect him.
The episode ends with Mulder and Scully realizing the enormity of the threat they face, with William's role in the future uncertain.

Nothing Important Happened Today

9x01
The Super Soldiers continue their infiltration of the government, working to advance the colonization plan.
Scully becomes increasingly worried about William, as his powers start to manifest more clearly.

Nothing Important Happened Today II

9x02
Mulder goes into hiding, believing that William's safety depends on it.
The Super Soldiers are shown to be nearly indestructible, making the fight against colonization seem even more hopeless.

Trust No 1

9x06
Mulder remains in hiding, while Scully is contacted by others who want to exploit William's powers for their own ends.
The episode highlights the growing danger to William from various factions, all interested in his potential as a human-alien hybrid.

William

9x16
Scully faces a heartbreaking decision as she gives William up for adoption, hoping to protect him from those who would use him for the alien colonization effort.
The episode suggests that William's powers have been suppressed, but his true nature remains uncertain.

The Truth

9x19
Mulder is put on trial for the murder of a Super Soldier, but the trial is a farce, designed to silence him.
The full extent of the alien colonization plan is revealed.
The date of the alien invasion is set: 12/22/2012.

The old syndicate has been replaced by a shadow government made of supersoldiers, like the toothpick man.

Mulder and Scully are now fugitives.

My Struggle

10x01
Mulder and Scully are drawn back into the X-Files by Tad O'Malley, a conspiracy theorist who claims to have new evidence of an alien-government conspiracy.
Mulder begins to question his previous beliefs, suspecting that the conspiracy is more about human experimentation and less about alien colonization.
The idea is introduced that the government has been using alien technology to conduct experiments on humans, manipulating global events.
The episode reintroduces the Cigarette Smoking Man, revealing his continued involvement in the conspiracy.

My Struggle II

10x06
Scully discovers that her DNA contains alien material, making her immune to a global pandemic being unleashed by the government.
The episode suggests that alien DNA has been secretly implanted in select individuals as part of the Syndicate's plan.
Mulder becomes gravely ill, indicating that the virus targeting the population is part of the government's depopulation agenda.
The episode ends on a cliffhanger with Mulder near death and an alien spacecraft appearing over Washington, D.C., hinting at the larger alien threat.

My Struggle III

11x01
The episode reveals that the events of "My Struggle II" were a vision experienced by Scully, who is now in a coma.
Scully awakens with renewed determination to find William, her and Mulder's son, who is believed to be the key to stopping the global conspiracy.
The Cigarette Smoking Man reveals that he is the true father of William, having manipulated Scully's pregnancy through alien DNA.
Mulder and Scully continue to chase down leads about the Syndicate's plans, focusing on finding William before the conspiracy fully unfolds.

My Struggle IV

11x10
The episode concludes the "My Struggle" arc, with Mulder and Scully racing against time to stop the Cigarette Smoking Man and his plans for global depopulation.
William, now a young man with powerful psychic abilities, becomes the focal point of the struggle between the forces of good and evil.
Mulder confronts the Cigarette Smoking Man, who is ultimately killed, seemingly ending his decades-long manipulation and control over the conspiracy.
William disappears, leaving his fate uncertain, while Scully reveals that she is pregnant with Mulder's child, offering a glimmer of hope for the future.
The episode closes with the possibility that the alien conspiracy is not entirely over, as William's whereabouts remain unknown, and his role in the broader scheme is still unclear.

Pilot

1x01
- Virtual characters are referred to as VC's.
- VCs have implanted tracking devices that set off alarms when they leave the perimeter.

Inga Fossa

1x03
We learn that in the real world, Pinocchio seems to have suffered a severe burn on one entire side of his body.

Camera Obscura

1x09
We learn that Harsh Realm went online on October 13, 1995.