After the events of The X Files (1998) movie, Mulder and Scully's new boss, Kersh, assigns agents Spender and Fowley to work on the X-Files instead of them. Ignoring this, Mulder takes Scully on a hunt for a rampaging alien.
An new, violent kind of alien that developed from a mutated alien virus is on the loose in Arizona. Mulder and Scully get reassigned from the x-files while Agents Spender and Fowley become the new agents in charge of the x-files. Mulder and Scully go to Arizona without permission to search for this new alien.—Muldernscully