The death of Scully's father figures prominently in Beyond the Sea, an episode in which the agents must scrutinizie claims of psychic powers by a convicted murderer. Brad Dourif is memorable as Luther Boggs, the death row inmate who seems to possess intimate knowledge of another madman poised to strike again if he is not caught.

In E.B.E., Deep Throat resurfaces to inform Mulder about a U.F.O shot down while flying over Iraqi airspace. The agents' faith in their informant is put to the test when he deceives them, hampering in their investigation. This episode also introduces Frohike, Langly, and Byers--collectively known as the Lone Gunmen--three paranoid hackers whose conspiracy theories fuel Mulder's own search for "The Truth.".