Season synopsis
Contains spoilers for this season and earlier seasons.
FBI agent Dana Scully is assigned to evaluate Fox Mulder’s work in the X-Files unit, where he investigates cases the Bureau cannot explain. Their first case follows apparent abductions in Oregon: Billy Miles, a comatose teenager, carries another abductee into the woods, while Scully finds a metallic implant during an autopsy. Mulder’s search also returns to the disappearance of his sister Samantha, which began when they were children; the season offers fragments and parallels, not a resolution. The agents’ investigations take them from an Arctic base where an organism drives researchers into violence to a forest where an ancient insect swarm traps a logging crew. In another case, Mulder identifies Eugene Tooms as a liver-eating killer who can squeeze through narrow openings; Tooms is released from a sanatorium, kills his psychologist to obtain the final liver he needs, then is trapped and killed beneath a shopping-mall escalator by Mulder.
A larger conspiracy takes shape through Deep Throat, a government insider who gives Mulder information while warning him about its cost. In the finale, a fugitive with green blood leads the agents to Dr. Berube’s secret experiments, where terminally ill volunteers have been exposed to extraterrestrial material. Scully confirms that a sample contains bacteria unknown on Earth, but the evidence disappears and witnesses are killed. Deep Throat helps her enter a secure facility and recover an alien fetus for a trade; the Crew Cut Man shoots him after the exchange. Mulder survives captivity, then learns that the FBI has closed the X-Files and reassigned both agents. The Smoking Man places the fetus in a Pentagon evidence vault, keeping the conspiracy hidden while the partners’ work is formally ended.