As Mulder takes in the words told to him by Michael Kritschgau, that extraterrestrial life is nothing but a hoax, he is contacted by Kritschgau telling him that someone may be watching Mulder's apartment. Later, Mulder arrives at Scully's apartment, informing her that the man who was watching Mulder for someone at the FBI is now dead. The two work around the clock in order to connect the dots to a mole inside the Bureau.

While Scully is lingering near death and the future of the X-Files in danger, Mulder is brought before Section Chief Blevins to explain the incident that led up to the hearing on his supposed death. When Skinner confronts Mulder, the agent tells his superior the truth about Scully's abduction.

In 1989, a straight-laced federal employee, a sex mad AV expert and a nerdy computer hacker meet Susanne Modeski, who claims to have evidences of a government conspiracy and is being followed by an FBI agent named Fox Mulder.

On their way to a FBI convention in Florida, Mulder and Scully involve themselves in a case where three men have mysteriously vanished in a large forest. Evidence at the crime scene seems to suggest someone human who walks on the balls of their feet.

Mulder and Scully head to a small Midwestern town to investigate reports of a two-faced monster that has been impregnating women.

Scully is haunted by dreams which hint at a strange connection to a murdered woman's daughter who bears an uncanny likeness to her sister, Melissa, at that age.

While Scully fights to protect Emily from the same men responsible for her adoptive parents' deaths, DNA testing on Emily reveals that she is actually Scully's daughter.

Mulder and Scully must race to catch an old adversary who has escaped from prison before he takes revenge against Mulder.

When a teenage boy is suspected of killing his father by burying him alive, Mulder and Scully head to Michigan to examine the death. The father was more than twice the size of his son and evidence is found that the boy could have had help. However, Mulder believes that the boy is innocent.

On a mini-vacation to Maine, Scully encounters bizarre cases where the victims appear to have inflicted wounds upon themselves. Evidence in the first case suggests a connection to a woman who has been suspected by the townsfolk of being a witch.

Mulder and Scully investigate the strange death of a computer genius. Unknown to them, a super-intelligent virus program is let loose on the Internet and begins to grow and expand by itself.

Having to give a report to Assistant Director Skinner on their latest case, Mulder and Scully both give each other their interpretation of the events that led to Mulder killing a man who he suspected was a vampire.

A series of horrific mass killings leads Mulder to startling evidence of extraterrestrial life. Meanwhile, Scully finds herself forming a special bond with Cassandra Spender, who is an abductee too.

At a third abduction site, one that Scully is summoned to, aliens once again set the gatherers on fire. Cassandra Spender has disappeared and her son, Jeffrey, blames Mulder for it.

Mulder visits a former FBI agent named Arthur Dales, who may be able to shed some light on why a murder suspect's last word was the young agent's name. Dales tells him a story about the agents assigned to a would-be X-File in the Cold War era of the 1950's.

Mulder and Scully investigate a murder where the main suspect is a blind woman but Mulder suspects that her involvement is not what it seems.

A priest asks Scully to investigate the unexplained death of a disabled young girl, but her investigation leads her to face a mystery that even she is afraid to understand.

Scully begins to suspect Mulder of having another agenda while they are investigating a dangerous group of anti-government terrorists experimenting with biological warfare.

Mulder and Scully are instructed by Skinner to assess the threat at a telemarketing center in Illinois. A similar incident has happened before and this time a manifesto was sent to a Chicago radio station with claims of a paranormal nature at the center. Feeling that the case is a waste of time, Mulder tells Scully to stay behind while he plays the good Bureau kicking boy. However, Mulder soon realizes that the case is actually an X-File.

An attempted assassination of a young boy with psychic powers draws Mulder and Scully into an investigation that strikes at the heart of the X-Files.