Agent Dana Scully is assigned to work with Agent Fox Mulder on the X-Files in an attempt to debunk his work on the paranormal. Their first case has them investigating apparent alien abductions. A near comatose man, Billy Miles, is taking his classmates, including Theresa Nemman, into the woods, where they are killed in a flash of bright light.

Mulder & Scully travel to Idaho in order to investigate the disappearance of a military test pilot. They observe unusual aircraft activity, prompting Mulder to proclaim the existence of a government conspiracy. Mulder sneaks onto the military base and is spotlighted by one of the craft, but is captured by soldiers and has his memory erased before he is released.

Mulder and Scully investigate a series of murders where there appears to be no tangible method for the murderer’s entrance and escape. Eugene Tooms, a seemingly normal janitor, is suspected by Mulder to be a mutant who kills his victims and extracts their livers in order to prolong his existence.

As Section Chief Blevins expresses his concern with the direction of the X-Files department, Mulder becomes obsessed with solving a case that closely parallels an ‘encounter’ he experienced as a child... the abduction of his younger sister, Samantha.

The murder of a homeless man which is very similar in detail to a murder committed in 1947 leads Mulder and Scully to a legendary man-beast roaming in the forest near Atlantic City.

When an unseen force commits several murders where a young woman is present, Mulder suspects that it is the spirit of the woman’s former boss who was believed to have committed suicide but was actually murdered and he is protecting her from his business partner.

A computer with highly advanced artificial intelligence begins to kill in order to preserve its existence when it is deemed inefficient to continue controlling the workings of an office building.

When an Arctic research team mysteriously kill each other and themselves only days after drilling deeper into the ice than ever before, Mulder and Scully accompany a team of doctors and scientists to investigate. They discover an organism which infects living creatures and amplifies the host’s feeling of anger and paranoia, and the new team starts to deteriorate as they wonder who among them are killers. "Bring your mittens."

A mysterious force is sabotaging a space launch program which leads directly back to the commander of the team, who once claimed to have seen an alien in space while witnessing Mars from Earth orbit.

Mulder puts the future of the X-Files in jeopardy when he heads to a UFO crash site being rapidly covered up by the military. He is arrested and while in jail he meets Max Fenig, a UFO nut whose NICAP group has followed Mulder’s work on the X-Files. When Mulder is released, Scully urges him to return to Washington to face his superiors and try and save his job but Mulder finds out that Max is more than meets the eye and ignores Scully to try and save him instead.

When two fathers on opposite sides of the country are unexplainably murdered at the exact same time in the exact same way, Mulder and Scully find that their eight-year-old daughters are perfect twins and were created in order to continue The Litchfield Experiment, a eugenics project of the 1950’s which produced cloned boys named Adam and girls named Eve who have heightened strength and intelligence, but are prone to psychotic behavior.

Mulder investigates the deaths of British dignitaries at the behest of an old Oxford girlfriend. Bob/Cecil L’Ively is a pyrokinetic, and he wants Sir Malcolm Marsden’s wife. Cecil attempts to kill Marsden, with his ability to make fire come out of his hands, but Mulder stops him.

A death row inmate named Luther Lee Boggs claims that he is psychic and can lead Mulder to a serial killer in exchange for a lesser sentence of life in prison. The agents’ roles are reversed in this episode, with Mulder doubting Boggs’ claim and Scully believing him after she is told that she can communicate through him with her recently deceased father.

• First appearance by Sheila Larken as Margaret Scully.

A series of identical sexual murders, where the killer appears to be both male and female, draw Scully and Mulder to an Amish-type community of people who may be alien in origin.

When FBI Agent Jack Willis and bank robber Warren Dupre are both shot at the same time during a robbery attempt, Dupre dies when Willis is brought back to life. When Willis rushes out of the hospital and begins acting strangely, Mulder concludes that Dupre has come back to life in Willis’ body.

A psychotic criminal from one of Mulder’s past cases - John Barnett - is back to get revenge on Mulder for incarcerating him. Before Barnett’s release, a renegade doctor had found a way to reverse the aging process - using Barnett as his test subject. Mulder and Scully rush to catch the now-unrecognisable youthful Barnett before he carries out his threat to kill all of Mulder’s loved ones.

Mulder and Scully receive information from Deep Throat about a UFO that was shot down over Iraq and has been secretly transported to the US. However, Deep Throat then intentionally misleads the agents to prevent them from discovering the truth.

• First appearance of The Lone Gunmen.

Mulder and Scully travel to Tennessee to investigate the “Miracle Ministry” and its star attraction - a young man with the ability to heal people with his touch - when a person dies shortly after being healed. As more people start dying, the agents must unravel the earthly from the divine.

Mulder and Scully head to an Indian reservation in northwestern Montana to investigate a manslaughter case which Mulder believes may relate to the very first X-File ever created at the FBI, and its main subject: Lycanthropy.

Mulder and Scully travel to the remote Washington State National Forest when an entire group of loggers goes missing.

Eugene Victor Tooms (see “Squeeze”) is released from the psychiatric sanitarium in which he was incarcerated for assaulting Scully - and he needs to kill once more to get the final liver which will allow him to hibernate for another thirty years. Mulder and Scully race against time to find evidence of his involvement in the past string of murders before Tooms disappears again.

• First appearance by Mitch Pileggi as A.D. Walter Skinner.

After a detective and his former partner die in unexplained circumstances, the accidents are linked to a little girl who witnessed both deaths and Mulder believes that she may be the reincarnation of a policeman murdered by his colleagues.

Agents Mulder and Scully investigate series of murder in Mahan Propulsion Laboratory as a team of scientists die one by one and the only suspect is a mentally handicapped cleaner named Roland.

A seemingly unrelated car chase leads Mulder and Scully to a scientific lab encompassing a secret which could provide proof of a government conspiracy. However, individuals involved with the scientific experiment are being murdered, and the two agents must ensure their own safety. The two come across a flask containing strange DNA particles. All living things are built up of a string of four different DNA nucleotides, but this flask contains bacteria infected with a virus that uses a fifth and a sixth. Scully and Mulder believe that this could be firm evidence of extra-terrestrial life forms. Scully also finds a small head sized alien fetus- which changes her beliefs completely. At the end of this episode, the X-Files project is aborted.

With the X-Files shut down, Mulder finds his own belief in the truth waning. So when an old political ally gives him a new reason to believe, he goes alone to an abandoned SETI program site -- Arecibo Observatory -- in Arecibo, Puerto Rico. Concerned for his safety, Scully has to track down his whereabouts before someone or something else does.

When a man’s decomposed body is found in the sewers of Newark, Mulder is given the supposed “grunt” work. But after Scully’s autopsy turns up a parasite living inside the body and a sewer worker is attacked and bitten by something, it opens up a whole new can of worms.

A recent rash of killings in the small town of Franklin, Pennsylvania brings Mulder to profile the murderers — a task made more difficult by the fact that none of them had any previous history of violence and all died at the end of their berserk rages. The only clues he has are some destroyed electronics and an unknown organic substance. The events lead to the discovery of a bizarre experiment on the town.

An audio cassette hidden in his morning paper brings Mulder to request the case of a scientist’s death consistent with burning, despite the lack of any evidence of any flames or burns. He is given his request...along with a new partner, Agent Alex Krycek.

• First appearances of Steven Williams as X and Nicholas Lea as Alex Krycek

An ex-FBI agent escapes from a mental hospital and holds several people hostage in a travel agency. Mulder and Krycek are sent in to help with the negotiations since the man claims to have been a UFO abductee.

A.D. Skinner reopens the X-Files, but Mulder is finding it difficult to work without the missing Scully. When he recognises a Los Angeles killing as the work of the Trinity murderers, a trio of killers with a fetish for drinking blood, it gives him work in which to immerse himself.

When Scully mysteriously re-appears comatose in hospital, Mulder drives himself crazy trying to find the people responsible. Though his quest for vengeance could make him exactly like those whom he despises.

A malfunction in a robot designed for volcanic exploration yields evidence of a lifeform living in the caves. When this lifeform seemingly causes the death of a member of the research team, Mulder and a newly returned Scully are flown out to the site to investigate before anyone else dies.

Mulder and Scully’s latest case begins with the rape and battery of a nurse in a Massachusetts convalescent home. What makes it an X-File is her claim that her attacker was invisible. But upon their arrival, they discover that the unrest is not limited only to the live – in residents.

The body of an old FBI agent is unearthed in Aubrey, Missouri. A serial killer is also on the loose in Aubrey. Mulder and Scully must determine the killer’s identity with Lt. Tillman.

A female corpse, dug-up and mutilated, is brought to Mulder’s attention by a Minnesota agent claiming it as the work of aliens. Mulder believes otherwise and is vindicated when a similarly mutilated prostitute is found. But while he gets down to business, the case begins having a disturbing effect on Scully.

New Hampshire teenagers feign an occult ritual in an attempt to score and inadvertently cause the murder of one of their group. When Mulder and Scully are called to look into the matter, the town’s real worshippers attempt to hide their tracks, though they fear that the boys’ attempt to “get some” got them more than they thought.

When a soldier stationed at a resettlement camp for Haitians drives himself into a tree, Mulder and Scully are called by the grieving and fearful wife. Her fears of a voodoo curse seem only to be reinforced by the beliefs and actions of many of the local residents, including a few of the other soldiers.

A newspaper ad placed to locate a certain doctor sets off the murder of several people with the same face. When Scully and Mulder locate another look -alike, they work to find him before the killer does. Coming to Mulder’s aid is another familiar face, but one he wasn’t expecting. Samantha, Fox’s lost sister, and his father, William Mulder, appear in this episode.

• First appearances of Peter Donat as Bill Mulder and Rebecca Toolan as Teena Mulder.

Reeling from the reunion with his sister, Mulder is thrown into a quandary when Scully is taken captive by the bounty hunter. However, when a trap set for him goes awry, the agents must head far north in order to attempt to unravel the mystery.

The agents are called in when a boatload of survivors from a US Navy Destroyer are found. What particularly catches Mulder’s inquisitive eye is that all of these sailors appear to have aged many decades in the course of days.

Mulder and Scully must find the paranormal among the abnormal when they are sent to investigate a long standing series of ritualistic killings which match no known patterns. The latest of which was the death of the “Alligator Man,” just one of many sideshow acts around which the town of Gibsonton, Florida is built.

A photograph taken just before the death of a two year – old boy yields evidence of some supernatural intervention which piques Mulder’s curiosity. When another death in the family occurs, the grandmother of the remaining child requests the aid of some Romanian ritualists (called calusari, “horsemen”) in order to cleanse the home of evil.

An ex-student of Scully’s asks the agents to help her with her first investigation concerning a number of disappearances with very few clues. Mulder ponders the idea of spontaneous human combustion but rethinks it when they find a man who is afraid of his own shadow.

Dudley, Arkansas is the site of the latest investigation for Mulder and Scully, who are sent to find a missing poultry inspector. The case takes a twist when another poultry worker is shot after she goes insane, giving Mulder a hunch that the townsfolk really are what they eat.

The trust that Mulder and Scully have is sorely tested when Mulder begins acting strangely. His aberrant behavior is compounded when the Lone Gunmen direct him to a hacker who managed to break into some very closely guarded files. While Mulder’s investigation leads him to long-awaited answers, Scully finds her career on the line, and the Cigarette Smoking Man decides to take some action himself.
Guest starring: Floyd Red Crow Westerman as Albert Hosteen Cameos: Chris Carter as FBI interrogator near the beginning of the episode.

The Cigarette Smoking Man works quickly to recover the stolen computer files, but finds himself thwarted by a man whom he hoped was dead. Meanwhile, Scully finds herself at a loss for her next step and turns to her family for support, since Mulder is otherwise engaged fighting for survival.

• First appearance by John Neville as Well Manicured Man

Mulder and Scully search for answers regarding the old photograph with his father and other unnamed men. Their search takes them to the abandoned Strughold Mining Facility where they uncover a dangerous secret.

Mulder is skeptical over a coroner’s report regarding the fifth person to be struck by lightning in a small Oklahoma town. Their investigation into the latest death seems to point to the only person to have survived a lightning strike, an emotionally-charged youth.

Skeptical of a famous psychic’s predictions regarding the murder of several prognosticators, Mulder instead finds someone who he believes truly can predict the future. Catching the killer could prove difficult, though, particularly if the murderer can also see into his future.

• This episode won two Emmys. One was for the writing, and the other was awarded to Peter Boyle for his guest appearance in this episode.
• This episode was named the 10th greatest episode in TV history by TV Guide.

A death row inmate makes good on his promise to come back from the dead and kill the five people involved in his death. The fear of his retribution has everyone scrambling to determine if they are on the list, while Mulder and Scully attempt to determine how he has returned to execute his tormentors.

Meeting insecure women through an on-line service, a serial killer seduces his prey with the right words. However, Mulder and Scully determine these killings are far from ordinary by the presence of a strange substance coating the victims, a substance which seems to digest the fatty acids in flesh.

Another failed suicide attempt by a patient in a military hospital interests Mulder with the talk of a “phantom soldier” which has prevented the man’s death. The general in charge is at first opposed to the FBI’s involvement until the invisible killer begins stalking him. But none believe when the primary suspect is a quadruple amputee.

When a young girl is kidnapped from her home, a fast food worker miles away collapses on the job, apparently experiencing exactly what the child is feeling. When Mulder learns that the woman was kidnapped and held hostage for years as a child, he begins to believe that she may be the key to help find the missing girl.

A mail order videotape of an alien autopsy blossoms into a much more complicated investigation when Mulder and Scully find the distributor of the tape murdered in his own home apparently by a high-ranking Japanese diplomat. While Mulder’s search for the video leads him to a train car, Scully investigates a Mutual UFO Network group and discovers several women who claim to know her.

Scully takes X’s advice to heart and investigates more into the implant she removed from her neck. Mulder, having ignored the advice given him, finds himself trapped on the train with a Japanese scientist and the man sent to kill him.

Mulder tracks a series of religiously motivated murders. Each of the eleven victims claims to have been stigmatic but all turned out to be frauds. When Mulder and Scully discover a little boy displaying inexplicable wounds of religious significance, they try to protect him from the killer they know will be coming.

A small town is plagued by deaths in which the bodies are found covered in cockroaches. Working from home, Scully has scientific explanations for all of them but Mulder — at the crime scene with an attractive bug expert — suspects the insects may not be organic, or earthly.

Agents Mulder and Scully visit a small town to investigate a series of bizarre deaths, mainly among high school teenagers. Evidence points to a Satanic cult. Moreover, people in this village, including Mulder and Scully, seem to be changed by the events — the weak and aggressive features of a person’s character are turned inside out. Mulder drinks, Scully smokes, a peace-loving school director becomes leader of the mob. Eventually Mulder notices some coincidence with strange astrological phenomena, and two teenaged girls turn out to be main suspects as a consequence.

Agents Mulder and Scully join Mulder’s former mentor, the FBI’s chief profiler, on a case involving a serial killer who claims to be possessed by a demonic force. The case gets even more mysterious when the suspect is apprehended and the murders continue. Mulder gets involved more deeply than expected and Scully as well as Skinner are deeply concerned.

When a French salvage ship sends a diving crew to recover a mysterious wreckage from World War II, the crew falls prey to a bizarre illness and Agents Mulder and Scully join the investigation. The investigation leads to the discovery of a familiar face, and to Skinner's life being threatened.

While Mulder continues to investigate a bizarre illness that originated with the discovery of a mysterious World War II wreckage buried at sea, several government figures try to thwart their efforts. And as Skinner recovers from his shooting, Scully discovers that he is still in danger, from the man who killed her sister.

Agents Mulder and Scully’s assistance is requested for a case involving a man seemingly capable of bending people to his will. The suspect uses his mysterious abilities to manipulate Agent Mulder into a dangerous end game.

A series of deaths occurs immediately after an ancient artifact is brought to Boston from an excavation site in South America. According to Scully, the deaths appear to be the result of political terrorism, but Mulder suspects something more improbable.

A string of mysterious deaths of recent Chinese immigrants brings Agents Mulder and Scully to San Francisco’s Chinatown. The Agents team up with a Chinese-American detective to better understand the language and customs of the Chinese culture, but one thing remains frightening clear — all of the bodies are missing various internal organs.

When a couple claims to have been abducted by aliens, Agents Mulder and Scully try to get at the truth but everyone has a different version of the story, including the “aliens” themselves.

During a difficult time in assistant director Skinner’s life, he meets a woman in a bar and spends the night with her. The next morning, the woman is dead and he is accused of murder. Agents Mulder and Scully join the investigation to clear their supervisor’s name. As they unravel the threads of a conspiracy, they also learn more about Skinner’s personal affairs.

When a series of mysterious deaths and disappearances are reported near a lake in a small town, Agents Mulder and Scully are called in to investigate. With local folklore of a killer sea serpent running rampant amongst the locals, the agents must take their search for the truth to the water.

Agents Mulder and Scully uncover a dark conspiracy behind a bizarre series of seemingly unrelated murders in a small town. As the extent of the conspiracy is revealed, Scully's trust in Mulder is put to the test. Eventually, even Scully shows the symptoms of a severe psychosis leading to paranoia. She believes Mulder has moved to “the other side” and betrayed her and may even want to kill her. In the end, Mulder is led into a conflict between revealing his “contact” and providing the secret, but keeping the last murder unrevealed.

Agents Mulder and Scully search for a man who seems to possess strange powers, which leads to the discovery of a dangerous secret from Mulder’s past. The secret could bring Mulder and Scully to the brink of exposing the truth about alien existence.

The traditional opening credits text reads “The truth is out there”; however, in this episode, it reads “Everything dies”, a phrase spoken by the Alien Bounty Hunter to Mulder. Later in the episode, Marita Covarrubias, in her first appearance of the season, tells Mulder that “not everything dies”. While Mulder and Jeremiah Smith attempt to uncover the truth, the Syndicate realizes that they have a traitor in their midst. The informant known to fans as X dies in this episode, as he is discovered to be the source of the leak. As he dies, he scrawls the letters SRSG on the floor of Mulder’s apartment in his own blood. Later, it is implied that these letters stand for Special Representative to the Secretary General, and lead Mulder to Marita Covarrubias (who is the SRSG’s assistant).

• Herrenvolk means Master race in German.

Mulder and Scully travel to the rustic small town of Home, Pennsylvania where they find evidence of an unspeakable crime.
Guest starring:Tucker Smallwood as Sheriff Andy Taylor
Sebastian Spence as Deputy Barney Paster
Karin Konoval as Mrs. Peacock

The mysterious deaths of several African-American men whose skin color has turned white sends Mulder on a quest into African folklore.
Guest starring: Willie Amakye as Samuel Aboah
Carl Lumbly as Marcus Duff

Agents Mulder and Scully investigate a group of bizarre abductions in which the only clues are inexplicable photographs. But when Scully is the next intended victim, Mulder must get into the killer’s head.

Agent Mulder’s search for an informant inside a cult compound leads Scully and him to one of the cult leader’s wives. What they soon discover is an unexpectedly close connection with the woman.

Bizarre murders in a hospital’s plastic surgery unit lead Mulder and Scully to suspect a supernatural force may be responsible.

Taking a page from the Superman comic “Lex Luthor: The Unauthorized Biography,” this episode details the previous exploits of the Cigarette Smoking Man. Mulder, Scully and Byers meet with Frohike, where he details what may be Cancerman’s real life.

A diplomatic courier carrying deadly cargo involves Agents Mulder and Scully in a dangerous web of intrigue, which leads Mulder on a trip to Russia.

Scully and Skinner attend a suspicious Senate hearing, while Mulder and Krycek face off in a Russian gulag.
The phrase "E pur si muove" that is shown instead of the "The Truth is out there" means "And Yet it Moves." This comes from a legend that famous philosopher Galileo Galilei muttered this phrase after being forced to recant his belief that the earth moved around the sun in 1633, before the Inquisition. "Galileo Academy of Science and Technology". Retrieved on 2007-07-29.

Agent Mulder is haunted by an old case in which young girls were killed and hearts cut from their nightgowns, Soon Mulder becomes suspicious when the killer taunts him with the idea that one of his victims may have been Samantha.

Deadly rain in a migrant workers camp sends Agent Mulder and Scully on the trail of a mythical beast — El Chupacabra.