The story takes place somewhere within the third season timeline of The X-Files. It follows Craig Willmore, a young FBI agent in Seattle, who is assigned by Assistant Director Walter Skinner to investigate the disappearance of Fox Mulder and Dana Scully, last seen in the Everett, Washington area.

Willmore uses spy tools including night vision goggles, a digital camera, a PDA, lock picks, an evidence kit, a standard issue handgun, handcuffs, and a badge as he follows their trail. He is partnered with Seattle Police Department detective Mary Astadourian, and a minor subplot involves a relationship developing between them.

Several actors from the television series reprise their roles, including David Duchovny, Gillian Anderson, Mitch Pileggi, Steven Williams, Bruce Harwood, Tom Braidwood, Dean Haglund, and, depending on the outcome, William B. Davis. The plot involves aliens taking over human bodies and includes references to the show’s extraterrestrial mythology.

The game is set and was filmed in Seattle. Its screenplay was written by Richard Dowdy, Greg Roach, and Frank Spotnitz, from a story by Chris Carter and Frank Spotnitz.