Special Agent Dana Scully is partnered with Special Agent Fox Mulder to validate his work on a special project called the X-Files. While he is a believer in the paranormal fueled by a lost memory of his sister's abduction, she is a scientist and prefers to look for rational, logical explanations. Their first case takes them to Oregon to investigate the unsolved murders of several High School classmates who "Spooky" Mulder believes have been experimented on by aliens.

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.

One of Scully's friends from the FBI academy, now working in the Violent Crimes Unit, asks her to assist him on a homicide investigation involving no clear point of entry. Mulder realizes that this is similar to a series of X-Files cases that have occurred every thirty years and joins in the investigation to stop the latest cycle.

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.

The murder of a homeless man that 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 protecting her, while Scully believes the boss merely faked his own death.

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 members of 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 that infects living creatures and accelerates the hosts' feelings of anger and paranoia, and the agents' colleagues on the expedition begin to question their government knowledge.

A mysterious force is sabotaging a space launch program, which leads directly back to the commander of the team who once led a mission to Mars and claimed to have seen an alien in space.

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.