The Lone Gunmen request Mulder and Scully's assistance in a murder case at a video game company. A virtual reality game has gone haywire, and players are dying for real at the hands of Maitreya, the central character in this game. Mulder and Scully enter the game in an attempt to find and stop the killer.

Two U.S. marshals, several street-level criminals, and a computer software pioneer (Donald Gelman) are all casualties of a bizarre diner shoot-out in the middle of the night. The Lone Gunmen help Mulder and Scully track down Invisigoth, a computer hacker who knew Gelman. She informs them about an artificial intelligence program created by Gelman that has deadly intentions. The only way to stop it is to feed it the "kill switch", a CD containing a neutralizing virus.