In Africa, Scully searches for answers for Mulder's condition by studying rubbings taken from the fallen spacecraft. Back in D.C., Skinner tries to help Mulder by finding Michael Kritschgau at Mulder's request, who may know what is causing Mulder's accelerated brain activity.
Mulder's condition continues to deteriorate. He is kidnapped from the hospital by the Cigarette Smoking Man for insidious purposes. Mulder experiences dreams of another life, away from the x-files. Scully searches frantically for Mulder before it's too late.
At the turn of the 21st century, a religious fanatic enlisted by the Millennium Group resurrects four members of the group as zombies to bring about the end of the world. Mulder and Scully enlist the help of Frank Black to help stop the apocalyptic designs of the Millennium Group.
A man is tossed off the top of a 29 story building by gangsters. Amazingly, he gets up and walks away unscathed. Mulder and Scully investigate when Mulder suspects this man may have paranormal abilities. The man in question may just be the luckiest man on Earth.
Five years have passed since Scully escaped from Donnie Pfaster, an obsessed death fetishist. When Reverend Orison helps the madman get away from prison he immediately turns to the 'one' that got away...Scully.
Mulder and Scully investigate the apparent murder of a magician who was decapitated just minutes after he was able to perform the trick of turning his head around 360 degrees. The agents are perplexed when Scully discovers during the autopsy that the deceased died well before he performed his final trick.
A man is found dead in his locked car, killed from over a hundred snake bites. However, no evidence of snakes being present is found. The man was a former member of a religious cult that believes in snake handling. Mulder and Scully believe that this snake death was no accident, and that it may have been a murder involving this snake handling cult.
Mulder requests to be put on the case of a seemingly routine child abduction case of a missing little girl. Mulder finds a connection between this case and old x-files involving missing children. Scully believes that Mulder is personalizing the case, relating it to the abduction of his sister Samantha.
Mulder enlists the help of Harold Piller, a police psychic, to search for the missing girl, Amber Lynn LaPierre. Meanwhile, Scully searches for answers about Samantha's abduction, leading her to the Cigarette Smoking Man. Both of their investigations lead to Mulder finally learning the truth about his sister's disappearance.
The Lone Gunmen request Mulder and Scully's assistance in a murder case at a video game company. A virtual reality game has gone haywire, and players are dying for real at the hands of Maitreya, the central character in this game. Mulder and Scully enter the game in an attempt to find and stop the killer.
A boy is miraculously cured of his cancer, without medical treatment. After Scully visits the boy and his family, she is met by the Cigarette Smoking Man. He offers Scully the chance to obtain the cure for all cancer in exchange for going on a trip with him to get the cure and keeping the trip a secret from Mulder.
Mulder and Scully are on a stakeout of a female serial-killer of prostitutes. Mulder gets called away from the stakeout by Skinner to investigate the disappearance of federal judge's daughter. The strange appearance of a raven shortly before she went missing leads Mulder to believe this case may have paranormal significance.
Scully is finishing up the autopsy of a person at a hospital. A file mix-up involving the autopsy folder and another patient's x-ray leads Scully to discover a former lover of hers has been admitted at the hospital. Meeting with him again causes Scully to re-examine the decisions she has made in her life, leading to her where she is to today.
A potential witness in a high-profile tobacco case under Skinner's supervision, is found dead in his bathroom from mysterious circumstances. Skinner asks Mulder and Scully to assist him in the investigation. They find a man who smokes a unique kind of cigarettes, the second-hand smoke of which, has deadly results for the inhaler.
Skinner's buddy from college, Wayne Federman, trails Mulder and Scully on a case involving a pipe bombing in a church, at Skinner's insistence. Wayne is a writer/producer from Hollywood gathering material for a FBI-based movie. Mulder and Scully turn out to be the reluctant stars of this movie by Federman.
Two strikingly similar women, who do not know one another, cause people to erupt into violence upon each other, whenever these two women come in contact. Mulder and Scully set out to solve the mystery of this unexplained violence involving the two women.