Season synopsis
Contains spoilers for this season and earlier seasons.
After the previous season’s office fire and the intervening feature film, Mulder and Scully are removed from the X-Files. Agents Jeffrey Spender and Diana Fowley take charge, but the former agents pursue a new alien creature in Arizona. Cases send them from a ship lost in the Bermuda Triangle to Area 51, where Mulder and insider Morris Fletcher switch bodies. Scully discovers the switch before a time warp restores their original bodies. The agents return to their usual work, investigating a poisoned Assistant Director Skinner, a time-looping bank robbery and a planned community where rule-breakers disappear.
The conspiracy reaches a turning point in “Two Fathers” and “One Son.” Cassandra Spender returns as the first successful human-alien hybrid, bringing the colonists closer to launching their invasion. Mulder and Scully try to protect her as they uncover more about Jeffrey’s family and the Cigarette Smoking Man. The Syndicate prepares to hand Cassandra over, but faceless alien rebels attack and kill most of the conspirators. The Cigarette Smoking Man and Fowley escape; he later shoots Jeffrey Spender. Mulder and Scully resume the X-Files, though new questions remain about the aliens and their plans.
The finale begins with an inscribed artifact discovered on a beach in the Ivory Coast and the murder of the scientist who brings it to America. A rubbing of its symbols triggers severe headaches and apparent telepathic abilities in Mulder. Scully visits the dying Albert Hosteen in New Mexico, where the inscriptions are linked to biblical passages and human genetics. She returns when Mulder is hospitalized in a psychiatric unit, then follows the investigation to Africa. There she discovers a spacecraft partly buried on the beach, while Mulder remains confined and gravely ill.