Season synopsis
Contains spoilers for this season and earlier seasons.
The season opens by resolving the danger of the buried boxcar: Mulder is found alive in the desert and nursed back to health by Albert Hosteen. Scully continues investigating the files taken from the boxcar and discovers a program of human experimentation aimed at creating alien-human hybrids. Her sister Melissa is shot by assassins who mistake her for Dana and dies in hospital. Mulder pursues evidence of an alien autopsy and infiltrates a government train carrying what he believes is a hybrid, but a Syndicate operative nearly kills him before X intervenes. Scully’s own search for answers about her abduction brings her into contact with other women who report similar experiences and a Syndicate member called the First Elder. Elsewhere, an oil-like alien parasite discovered on a World War II submarine moves between hosts, eventually taking control of Krycek before escaping into a UFO.
The agents also handle cases that end within the hour: a man who foresees deaths helps them track a serial killer, while a writer’s investigation of reported alien abductions exposes how conflicting witnesses reshape a story. Those cases sit beside continuing pressure from the Syndicate and the unresolved questions around Mulder’s family. In the finale, a man named Jeremiah Smith revives victims of a shooting and disappears before Mulder and Scully can question him. Mulder’s mother suffers a stroke; a message she tries to write leads him to an alien weapon hidden in a lamp. The Smoking Man captures the real Smith, who can heal and change his appearance, while an impostor escapes FBI custody. Smith confronts his captor with the knowledge that he is dying of lung cancer. After escaping, Smith meets Scully and Mulder; Mulder wants him to heal his mother, but the Bounty Hunter arrives before they can leave.