This game is set during season seven of Aux frontières du réel (1993) television series and explains some of the loose threads from the show including the reason why the Smoking Man ordered the brain surgery on himself and Mulder in Amor Fati.
Street names in the game's first level, Red Falls, are all episode names from the television series. These include Ascension, Lazarus, Humbug, Conduit, Syzygy and Anasazi.
When recording their lines, the cast all wore the same red lipstick as seen in the "behind the scenes" clips that can be unlocked during the game or found in the game's submenus. Wearing lipstick while recording a voice performance is a common practice used to get better enunciation and crisper sound.
There is a villain in the game named John Gilnitz. John Gillnitz is an amalgamation of the names of show writers John Shiban, Vince Gilligan, and Frank Spotnitz. The name was used for seven characters throughout the shows run.
During the scene in the car in the opening sequence, Mulder quotes lyrics "Those fingers in my hair; That sly come hither stare..." to Scully. These are the lyrics to Frank Sinatra's song Witchcraft. Recognizing the lyrics, Scully replies that she gets the joke.