Scully helps Mulder fake his own death in order for him to go undetected through the Department of Defence and find out the answers to his new questions about the government hoax concerning the existence of extraterrestrial life. Meanwhile, at a joint FBI/DOD inquiry, Scully's attempt to drive out the Conspiracy's informant is halted as her cancer takes a bad turn.

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 Lone Gunmen 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.

While on their way to an FBI group communication seminar, Mulder and Scully manage to escape when they come across a situation in the Florida forest area where three men have recently disappeared.

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 murder 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?

A therapist working with children from abusive families is found to be implanting them with the memories of her own abuse suffered at the hands of her late father, when one of her patients tries to kill his stepfather.

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.

A super-intelligent virus program is let loose on the internet and begins to grow and expand by itself, eventually killing its creator when he tries to eradicate it.

After Mulder chases down and kills 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 is killed 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.

In 1990 Agent Fox Mulder visits an aging FBI Agent named Arthur Dales. He listens to a story of the agents assigned to a would-be X-File in the Cold War era of the 1950's and how Mulder's father was connected to a series of strange deaths.

Mulder and Scully try to get answers out of a stubborn blind woman found at a murder scene who may have the ability to look through the killer'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 is held hostage inside an office where a man claims his boss is a monster and has clouded all their minds while he turns them into zombies one by one, which is disbelieved until Mulder opens his mind and allows himself to see it too.

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