The agents' first case takes them to Oregon to investigate the unsolved murders of several high-school classmates.

Mulder and Scully head to Ellens Air Force Base to investigate the mysterious case of a military test pilot who disappeared after experiencing strange psychotic behavior. While on the case, Mulder meets a mysterious man dubbed 'Deep Throat' who claims to have classified information about his investigations into the paranormal.

Mulder and Scully search for a humanoid killer whose savage murder spree reoccurs every thirty years.

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

Mulder and Scully track a legendary creature that has roamed the New Jersey countryside for over forty years.

Mulder and Scully investigate the deaths of two men believed to have been killed by a powerful psychokinetic force.

It's Halloween, and Mulder and Scully are investigating the strange death of a corporate executive in a sophisticated high-tech building.

In the claustrophobic isolation of a remote outpost in Alaska, Mulder and Scully investigate the horrifying deaths of scientists.

Mulder and Scully are contacted by a communications specialist from NASA who shows them evidence of sabotage in the space programme.

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 to 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 inexplicably murdered at the exact same time in the exact same way, Mulder and Scully are called in to investigate. When they discover that the two fathers' eight-year-old daughters are identical twins, they realize that something even stranger is going on.

An old Oxford girlfriend of Mulder's asks for his help on an international case concerning the unexplainable execution of several British dignitaries, and they encounter an assassin who can produce fire from his bare hands.

When death row inmate Luther Lee Boggs claims to be psychic and can lead Mulder to a serial killer in return for a lesser sentence of life in prison, Scully becomes an unwilling believer when Boggs tells her that she can communicate through him with her recently deceased father.

A series of sexually-oriented murders, which are identical except that the killer appears to be both male and female, draws Scully and Mulder to an Amish-type community of people called the Kindred.

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.

Mulder becomes the target of someone from his past named John Barnett. He was a jewelry store robber with an itchy trigger finger that Mulder sent to prison when he first joined the Bureau. The only problem is that Barnett died four years ago.

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.

A young man who has the power to heal people with his touch begins to question his gift when people start dying after he has supposedly healed them.

Mulder and Scully travel to a Native American reservation to investigate the death of a man who was mistaken for a wild animal and may have been the legendary Manitou, a man who can shape-shift into a beast.

When a group of loggers in the Washington State National Forest disappear in the same way that another group disappeared 50 years ago, Mulder and Scully go along to investigate and find themselves trapped in a cabin surrounded by flesh eating insects that only attack at night.

Eugene Tooms is released from the sanitarium, and Mulder becomes personally involved to ensure that he is caught in the act of getting the last human liver he needs to go into hibernation for another 30 years.

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

Mulder and Scully investigate the death of a scientist working on advanced propulsion technology. The mentally challenged janitor Roland, who has secretly been completing the scientist's work, is the prime suspect.

When Deep Throat points out a news story about a fugitive who apparently drowned, Mulder and Scully cannot see what makes the case special but follow it up anyway. With Deep Throat's insistence, they discover evidence of a secret government project code-named Purity Control, which uses human test subjects and infects them with extraterrestrial DNA. However, the evidence and everyone who has seen it is quickly being eliminated.

With the X-Files closed, Scully has been assigned as an instructor at the FBI Academy while Mulder is doing menial surveillance work. After meeting with Senator Matheson, one of his supporters in regards to the X-Files, Mulder disobeys orders and heads to an abandoned SETI site in Puerto Rico which has inexplicably reactivated itself and could provide proof of contact with extra-terrestrial life.

A.D. Skinner sends Mulder to investigate a body which washed into the New Jersey sewer from the ocean. Mulder believes that the basic blue-collar assignment is punishment, but by Skinner's own admission, what he discovers is a true X-File.

When several violent deaths in a small farming community are connected by the destruction of digital devices, Mulder believes that people are being driven to kill by the use of subliminal messages in the digital readouts.

Mulder reluctantly accepts a new partner, Agent Alex Krycek, and they investigate the deaths of several Green Beret soldiers who participated in a sleep deprivation experiment during the Vietnam war.

Mulder is called to a hostage situation involving Duane Barry, a former FBI Agent who claims to be an alien abductee and wants to get back to the abduction site with someone who will be taken instead of him. Unfortunately, the someone he eventually chooses is Scully.

When Mulder finds out that Scully was kidnapped by Duane Barry, he risks the wrath of his superiors and the annoyance of Agent Krycek in order to do whatever it takes to find her. Meanwhile, Krycek is found to be reporting Mulder's activities to the Cigarette-Smoking Man.

Mulder, back on the X-Files but alone for the first time, investigates a series of vampire-like murders in Los Angeles and finds himself falling for the one woman that may be the prime suspect.

Scully mysteriously appears in a Washington hospital, alive but in a coma, and Mulder must fight to keep her alive in order to find out what happened to her and who did it to her. Meanwhile, Scully fights her own personal battle as she decides whether to stay or go on to the next world.

Mulder and Scully, reunited at last, head for an active volcano under a geological study and find a deadly life form that can survive in the searing heat of the crater and is killing the scientists to avoid being discovered.

While investigating the connection between the abduction of several teenagers and a rural religious cult, Mulder and Scully discover a secret test being performed on the children using the "Purity Control" alien DNA from 'The Erlenmeyer Flask' which leads Mulder to "the crew-cut man", Deep Throat's murderer.

Mulder and Scully uncover strange occurrences in an elderly care home when one of the nurses is attacked by an unseen force she claims to be one of the 90 year old residents.

When a detective mysteriously uncovers the remains of an FBI agent who disappeared in the 1940s while investigating a similar murder case to one she is now on, Mulder and Scully believe that the original killer had passed his genetic trait of violence to his grandchild.

A mortuary worker who gets his thrills from collecting hair and fingernails from the dead begins killing his soon-to-be collectibles himself and sets his seriously disturbed sights on Scully.

The ritualistic murder of a teenager in a small town gets Mulder and Scully caught up in a secret occult practice within the local school's PTA and a substitute teacher with strange powers.

While investigating several deaths and murders within a Haitian refugee camp, Mulder and Scully get caught in the middle of a secret war between the camp commander and a Voodoo priest.

After the obituaries of four identical men are e-mailed to Mulder, the agents are contacted by a shadowy CIA agent who tells them about a bounty hunter sent to wipe out the beginning of a colony of clones. Meanwhile Mulder is distracted by the sudden reappearance of his sister Samantha.

The alien bounty hunter kidnaps Scully and wants to trade her for Mulder's sister, who is revealed to be a clone herself. After the trade goes badly and Mulder discovers the truth about Samantha, he tracks the bounty hunter to his ship buried in the arctic ice and demands the whereabouts of his real sister.

In a small town in Idaho, a man is killed by what seems to be an invisible elephant. Mulder's investigation into the local zoo, its owners and a local animal rights group uncovers evidence of insidious alien experiments.

When half the crew of a Navy ship abandon their boat in a life raft and are rescued 18 hours later looking about 60 years older than they should be, Mulder suggests that the ship is caught in a time field which is speeding up their aging.

Mulder and Scully travel to Gibsonton, Florida, a town built and populated by circus and sideshow performers to investigate the death of Jerald Glazebrook, The Alligator Man. While searching for leads on the killer, the agents come across many bizarre characters including the local sheriff who was once known as Jim Jim, the Dog-Faced Boy.

The agents investigate when a young boy's family is plagued by a series of tragic accidents.

When a plague-like illness kills ten men inside a maximum security prison, Scully tries to get into the quarantine site and discover the cause and origin of the contagion, while Mulder and a group of US Marshals track two escapees who may be infected.

An experiment in dark matter accidentally turns a scientist's shadow into a deadly weapon that can unzip a person's molecules if they are touched by it.

After several disappearances in a small town, Mulder and Scully investigate and find hundreds of human bones in the river. They discover that the man behind the town's main source of wealth, a chicken processing plant, has found a way to prolong his life through cannibalism.

Mulder receives an encrypted computer disk containing the defense department's top secret files on extraterrestrial life and becomes a target. Scully takes him to a Navajo family that unearthed a buried secret to decipher the disk.