Set within the events of the third season of The X-Files, the game follows Craig Willmore, a young Seattle-based FBI agent played by Jordan Lee Williams. Assigned by Assistant Director Walter Skinner, Willmore is tasked with locating Fox Mulder and Dana Scully, who vanished while working in the Everett, Washington area. He carries a full investigator's toolkit—night-vision goggles, a digital camera, an Apple Newton PDA, lock picks, evidence collection gear, a standard-issue handgun, handcuffs, and a badge—and partners with Seattle Police Department detective Mary Astadourian, played by Paige Witte, whose relationship with Willmore develops as the case deepens.
Multiple cast members from the TV series appear in recorded performances: David Duchovny as Mulder, Gillian Anderson as Scully, Mitch Pileggi as Skinner, Steven Williams as X, and Bruce Harwood, Tom Braidwood, and Dean Haglund as the Lone Gunmen. William B. Davis appears briefly as the Smoking Man, his inclusion contingent on how the player resolves the game. Filmed on location in Seattle, the story centers on aliens capable of occupying human bodies. An in-game date of April 1996 places events after the season three episode "Avatar" and before "Wetwired." The screenplay was written by Richard Dowdy, Greg Roach, and Frank Spotnitz from a story by Chris Carter and Frank Spotnitz.