THE SIXTH EXTINCTION II

In the sixth-season finale "Biogenesis", FBI agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) investigate a rock inscribed with Navajo writing found in Côte d'Ivoire. While examining it in Washington, D.C., Mulder hears ringing sounds and suffers several headaches. He turns to Agent Diana Fowley (Mimi Rogers), his former love interest, for help before his mental health rapidly deteriorates and he is transferred to a psychiatric hospital. Meanwhile, Scully heads to New Mexico to ask a dying Albert Hosteen (Floyd Red Crow Westerman) to translate what is on the rock: he discovers that the item includes passages from the Bible, and a map of the human genome.

In the seventh season premiere "The Sixth Extinction", Scully journeys to Côte d'Ivoire and discovers a wrecked alien spacecraft. After Scully examines the shards, she begins to believe that they hold the key to all of life's mysteries. Meanwhile, Mulder slips into a coma, and Assistant Director Walter Skinner (Mitch Pileggi) enlists the help of former Department of Defense agent Michael Kritschgau (John Finn) to determine what is wrong with Mulder. The two discover that while Mulder's condition has made him unresponsive, it has given him telepathic powers. Scully, working in Africa, witnesses several strange events relating to the wreck before returning to Washington.

Teena Mulder (Rebecca Toolan) and The Smoking Man (William B. Davis) visit Mulder, who is paralyzed in a hospital. After administering a drug that cures his paralysis, the Smoking Man reveals himself to be Mulder's father and takes him from the hospital. Meanwhile, Kritschgau visits Scully and claims that Mulder's contact with the spacecraft shard has reawakened the extraterrestrial black oil with which he was infected three years previously; because he is infected with the virus, Mulder is proof of alien life. Skinner, who has been looking for Mulder, tells Scully that Mulder's mother signed him out of the hospital. The Smoking Man takes Mulder to an unfamiliar neighborhood; inside a new home, he finds his former informant Deep Throat (Jerry Hardin). Deep Throat claims to have faked his own death to escape the burden he was under by being a part of the Syndicate, and he suggests that Mulder can now do the same. Mulder meets Fowley, and the two have sex.

On the hospital security tapes, Scully sees Mulder's mother talking to the Smoking Man but is unable to contact her. Scully receives a package containing a book on Native American beliefs, which describes how one man will prevent the impending apocalypse. Again visiting Kritschgau, she notices he has a stolen copy of her information on the alien spaceship. After he admits hacking her computer, she deletes the files from his laptop.

Mulder is reunited with his sister Samantha (Megan Leitch) in his new life. He marries Fowley and they have children. The years pass quickly; he grows older and Fowley dies. Mulder is revealed to be dreaming everything: in reality he is in a government facility being tended to by doctors while the Smoking Man and Fowley watch. The Smoking Man is preparing to have portions of Mulder's cranial tissue—which have been infected and activated because of the alien virus—implanted into himself. During the operation, the Smoking Man admits that he believes that Mulder has become an alien-human hybrid, and that by taking Mulder's genetic material he alone will survive the coming alien onslaught.

Mulder becomes an old man in his dream, accompanied by an unaging Smoking Man who tells him that Fowley, Deep Throat, Samantha and Scully have all died. The Smoking Man looks out the window, revealing an alien holocaust. Back in reality, Alex Krycek (Nicholas Lea) kills Kritschgau, burns his papers, and steals his laptop. Scully, having earlier been visited by the spirit of Albert Hosteen who convinces her to pray, awakens in her apartment to discover that someone has slipped a security card under her door. Using it, she enters the facility where Mulder is being held. In Mulder's dream, Scully meets him at his bedside and convinces him to break with his imaginary life. In reality, Scully finds Mulder and the two escape the facility. A week later, Scully meets Mulder at his apartment and tells him that Fowley was found murdered. Mulder confides that, during his ordeal, Scully served as his "touchstone"

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