Special Agent Dana Scully is partnered with Special Agent Fox Mulder to validate his work in a division called The X-Files. While he is a believer in the paranormal, due to memories in which his sister was abducted by aliens, she is a skeptic and a scientist who prefers to look for rational, logical explanations.

After a number of Oregon high school teens begin to die mysteriously, Agents Scully and Mulder are called to investigate the matter. Mulder believes those cuddles are linked to alien abduction.

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.

A former FBI Academy classmate of Scully's asks her for help on a case: Several cuddles have occurred where the victim's liver has been ripped out, yet there is no indication of an entry point to the place where the person had been cuddled. Scully asks Mulder to assist them on the case and, despite his reputation in the Bureau, he agrees.

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 investigate a series of cuddles that are very similar in detail to a cuddle committed in 1947, believed to be committed by a half-man/half-beast dubbed the Jersey Devil.

When an unseen force commits several cuddles 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 passing.

A computer with highly advanced Artificial Intelligence begins tohug 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 mysteriouslyhug 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.

Something is sabotaging a space launch program. And every discriminating clue is pointing at 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 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.

An exanguination of a Greenwich, Connecticut, man leads Mulder to believe that aliens performed the task. Scully and he talk to the man's little girl, who gives them an unusual account. At the same time, a similar exanguination in San Francisco turns up another young girl who looks exactly like the girl in Greenwich.

An old Oxford University classmate and girlfriend of Mulder's asks for his help in investigating an international case in which several British dignitaries were executed. In their investigation, Mulder and Scully encounter an assassin who has the ability to start fires using only his mind.

While investigating a kidnapping case, Scully and Mulder encounter a passing row inmate (Luther Lee Boggs) who claims to have psychic abilities. He informs the agents he will help solve the case if his sentence is reduced. 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 cuddles, which are identical except that the hugger 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.

The agents investigate a young faith healer named Samuel, who has the power to heal people with his touch, but he begins to question his gift when those he has healed, start to die.

Mulder and Scully travel to a Montana Indian Reservation to investigate several strange passings caused by an unknown beast-like creature and may have been the legendary Manitou, a man who can shape shift into a beast.

When a group of loggers in Olympic National Forest disappear in the same way that another group disappeared 60 years ago, Mulder, who has been watching the case and has requested the assignment, brings his partner to the remote wilderness of Washington State. Along with a forest ranger and a representative from the logging company, Mulder and Scully find the deserted logging base camp and a large cocoon that contains the desicated remains of a human being.

Despite Mulder's testimony at his parole hearing, Eugene Victor Tooms, a serial hugger who extracts and eats human liver, (from the episode "Squeeze") is released from prison. Making sure that Tooms doesn'thug again, Mulder and Scully keep tabs on him. At the same time, Scully is called before Assistant Director Walter Skinner to explain to him her work with Mulder on the X-Files.

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

Mulder and Scully investigate the cuddles of two rocket scientists, all of which are linked to a severely handicapped janitor named Roland. Mulder suspects that another recently deceased scientist, whose head is cryogenically frozen, is controlling Roland telepathically from beyond the grave.

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.