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.

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

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 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 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.

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 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 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 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.

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.

Mulder and Scully investigate a series of human and cattle deaths by lightning and are led to a teenage boy who is the only survivor out of five people recently hit by lightning strikes.

An investigation into a video of an alien autopsy puts Mulder and Scully in the middle of a conspiracy involving WWII Japanese scientists brought to America to continue their experiments which may shed light on Scully's abduction.

A serial killer is captured after a three year manhunt, and he claims an evil spirit is responsible for the crimes. When the killings continue as he sits in jail, Mulder's battle with a former colleague gets more heated when he suggests that something more paranormal may be involved.

During a one-night-stand in the midst of his divorce, A.D. Skinner becomes a murder suspect, and Mulder and Scully return the many favors that he has done for them by analyzing evidence that someone doesn't want uncovered to prove his innocence.

After several African-American men are killed and the color is drained from their skin, Mulder learns about the Teliko, an African folktale about a creature who must suck the pigmentation from a persons body in order to survive.

After a Jewish man is murdered in a Jewish community, his killers are murdered, too. Mulder and Scully have to determine whether someone is exacting vengeance or larger forces are at work.

When a U.S. military general is inexplicably murdered in the back of his limousine, a paramilitary group is suspected. They believe it was a soldier who they liberated from a Vietnam POW camp and is plotting to kill certain corrupt military figures.

A case involving a strange old man warning two scientists of events in the immediate future which come to pass (and the use of their experimental flash-freezing compound that does not exist yet) has Mulder believing that one of the scientists has come from the future to stop his own scientific breakthrough from becoming reality.

After a swarm of bees mysteriously kill a postal worker in an enclosed restroom, Assistant Director Skinner covers it up by destroying the evidence. In order to complete the task he poses as Agent Mulder, however his deception backfires. When Mulder finds out and confronts him, Skinner reveals that he is working for the Cigarette-Smoking Man in order to obtain a possible cure for Scully's cancer.