In order to follow their trail, Agent Willmore must use a variety of tools along the way, including night vision goggles, a digital camera, PDA (an Apple Newton), and lock picks, as well as law enforcement gear such as an evidence kit, standard-issue handgun, handcuffs, and even his badge.

During his assignment he is partnered with a Seattle Police Department detective named Mary Astadourian (played by Paige Witte), and a minor romantic subplot involves a relationship developing between the two.

Several of the actors from the TV series reprise their roles in the game, including David Duchovny (Mulder), Gillian Anderson (Scully), Mitch Pileggi (Skinner), Steven Williams (X), Bruce Harwood, Tom Braidwood and Dean Haglund (The Lone Gunmen) and—very briefly and depending upon the outcome of the game—William B. Davis (The Smoking Man).

The game uses a point-and-click interface, uses full motion video technology called Virtual Cinema, and includes a large number of cut scenes.

Dubbed "UberVariables", certain decisions made by the player can set them along one of three tracks: Paranoia (Willmore will start seeing things like twitching corpses and shadowy figures), Loss (messages from his ex-wife are kinder), and "The X-Track" (more details are revealed about mytharc-related conspiracies).

A former U.S. naval base, at Sand Point, was used as the setting for the NSA facility at the end of the game, and the boat used as the Tarakan is a training ocean-going tug, which had previously been used in a drug smuggling plot.

The game was filmed on Digital Betacam tape with Sony cameras and captured using Power Macintoshes running Adobe Premiere and Media 100.

"[28] During the Academy of Interactive Arts & Sciences' 2nd Annual Interactive Achievement Awards, The X-Files Game was a finalist for "Computer Entertainment Title of the Year", "PC Adventure Game of the Year" and "Outstanding Achievement in Character or Story Development", although it lost these prizes to Half-Life, Grim Fandango and Pokémon Red and Blue, respectively.