As the show's fifth season ended, the X-Files had been shut down, and Mulder and Scully were assigned to other projects. The movie opens with them assisting Darius Michaud's FBI team staking out a building in Dallas which has had a bomb threat. They discover the bomb across the street but it explodes.

Through evidence given him by a paranoid doctor, Mulder grows to believe that the bomb was deliberately allowed to explode to destroy evidence of some victims of the alien virus. Despite the fact that he and Scully are in danger of losing their jobs at a hearing led by A.D. Jana Cassidy, and attended by A.D. Skinner, they pursue the evidence. But when Scully is stung by a bee infected with the virus, and is kidnapped, a desperate Mulder seeks her out. The Well-Manicured Man tells him where to find her, in Antarctica, and what the antidote is but in doing so, loses his life.

Mulder journeys to Antarctica and saves Scully, in the process discovering a secret lab run by the Cigarette-Smoking Man and his colleague Strughold. The lab is destroyed when the alien ship lying dormant comes back to life.

Later, Mulder and Scully give evidence at the hearing where Cassidy routinely ignores their remarks. At another outpost - in Tunisia - the Cigarette-Smoking Man learns that the X-Files office has been reopened...