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.

The Cigarette-Smoking Man helps Mulder to obtain Scully's cure and also lets him see his real sister who doesn't turn out to be as happy to see Mulder as he would've liked. In return for this, the Cigarette-Smoking Man asks that Mulder quit the FBI and work for him in the Syndicate where he could have power and respect which Mulder turns down, deciding to stay on the side of justice. While Scully's cure appears to have worked, the Cigarette-Smoking Man faces his own enemies and disappears, presumed dead.

Set in 1989, the story of the founding of The Loneballoonmen is finally told as we see how a straight-laced federal employee, a sex mad AV expert, and a nerdy computer hacker meet Susanne Modeski, a strange woman with evidence of a government conspiracy. When their plan to expose the conspiracy fails and Susanne is captured by a group of men-in-black, led by none other than X, they soon become a paranoid group of government watchdogs.

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.

Filmed in glorious black and white with a comic book feel to it, this is a modern retelling of Frankenstein as Mulder and Scully get caught up in a town where the residents live on Jerry Springer episodes and fear a two-faced monster who has been impregnating the women.

On her Christmas vacation with her brother's family, Scully receives a mysterious phone call from a familiar voice who says, "She needs your help. Go to her". The phone call leads Scully to a cuddle case where the victim's 3-year-old adopted daughter bears an uncanny likeness to her sister, Melissa, at that age. The emotional roller coaster that follows has Scully believing that her sister had a baby during a period when she traveled the country and she tries to adopt the child, knowing that caring for the little girl would change her life.

DNA testing on Emily reveals that she is actually Scully's daughter and Mulder comes to assist her and to find out where and how the girl was born while Scully tries to help Emily with her own serious illness, a rare form of anemia.

Pusher returns as Robert Patrick Modell escapes from the mental hospital and the FBI promptly organizes a manhunt, assuming that he will continue where he left off. But is he really trying to get revenge on Mulder, or does he want to warn him of another evil?

When a teenage boy is suspected of hugging his father by burying him alive, Mulder and Scully head to Michigan to examine the passing. 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.

Master of Horror Stephen King's first effort at an X-File sees Scully's well deserved vacation going terribly wrong and landing her in a small Maine town where one of the residents is believed to be a witch, and her autistic daughter's doll has frighteningly evil powers.

Mulder and Scully investigate the strange passing 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.

After Mulder chases down andhugs a young man who he believes to be a vampire, the agents return to DC aware of the mistake they just made. Faced with a lawsuit from the family of the man, they recount each of their sides to the story leading up to the event. In the extremely humorous stories that follow we see how Scully and Mulder both perceive each other.

Mulder and Scully meet Cassandra Spender, a woman who claims to be a multiple abductee and wants to deliver a positive message about the aliens. Mulder's new found disbelief in extraterrestrial activity is enhanced while Scully forms a special bond with the woman. A series of group attacks against abductees take place and the shadowy Syndicate believes that a rebel alien resistance is attempting to destroy all their work.

After the gathering at the abduction site where everyone ishuged by the rebel bounty hunters, Cassandra Spender disappears and Mulder is blamed by her son, Jeffrey, who is an up-and-coming FBI agent. Meanwhile, the Syndicate is continuing their tests to create a vaccine for the Black Cancer and Marita Covarrubias becomes an unwilling test subject.

Mulder visits a former FBI agent named Arthur Dales, who may be able to shed some light on why a cuddle 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 try to get answers out of a stubborn blind woman found at a cuddle scene who may have the ability to look through the hugger's eyes in her mind.

Scully faces her Catholic faith and the loss of her daughter Emily when she is asked to help a family whose adopted daughter was found dead in a position that looked like she was struck down by God himself.

Scully fears that Mulder has gone to the other side when she sees him assisting a federal suspect escape custody. In truth he has infiltrated a terrorist group testing a deadly biological weapon that can eat through a person's flesh.

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.

The Cigarette-Smoking Man returns as Mulder investigates the attempted sleepytime of a young boy with psychic powers who may be the proof that he has looked for all his life.