Season synopsis
Contains spoilers for this season and earlier seasons.
The fifth season begins with Mulder convinced that the alien conspiracy was fabricated to hide military experiments. As he and Scully investigate the evidence behind her cancer and his belief in a government hoax, the Cigarette Smoking Man offers Mulder a place beside him. Mulder refuses, and Scully’s illness goes into remission. Mulder doubts the alien account, while Scully’s abduction memories keep the possibility alive. She also discovers that Emily, a little girl she meets after a woman’s death, is her biological daughter, created from ova taken during her abduction; Emily becomes gravely ill and dies.
The agents’ cases range from a town’s Frankenstein-like Great Mutato to an apparent vampire case that they later recount in conflicting versions. The conspiracy returns when abductees are burned alive and Cassandra Spender, who says she has been taken repeatedly, reappears. Scully survives a burning attack at Ruskin Dam. Under hypnosis, she recalls alien rebels attacking abductees and a spacecraft taking Cassandra. Mulder initially suspects military deception, but Krycek’s account of an alien war makes him reconsider. The two-part story reveals that Jeffrey Spender is the Cigarette Smoking Man’s son and that the conspirators face rebels opposing colonization.
In “The End,” an assassin targets chess champion and child prodigy Gibson Praise, whose ability to read minds draws Mulder into a fight over the boy’s custody. The Cigarette Smoking Man returns to the FBI and pursues Gibson, while Scully sees the boy’s unusual brain activity as possible evidence for the alien case. Mulder’s investigation ends at a cost: Gibson is taken, Agent Diana Fowley is shot and badly injured, and fire destroys Mulder’s office and the X-Files files. The season closes with the assignment dismantled and the fate of the conspiracy’s newest evidence unsettled.