The name Rauch is used in both X-Files games - in the first FMV game (simply called The X-Files Game (1998) or X-Files: The Game) as the name of a villain, and in this game as the name of a shady biotechnology company first mentioned on the show in the season 4 episode Redux II.
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.
This game is set during season seven of The X-Files (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.
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.
Some of the fake movie posters in Red Fall's VHS store called the Wetwired Video have the names of several X-Files episodes on them as fake movie titles. These include Quagmire (the yellow poster featuring the aquatic dinosaur, Big Blue, from the episode), Field Trip (just left of the store's entrance) Amor Fati (red poster) and The Host (black and yellow poster next to the Amor Fati poster). One of the posters that's not based on an episode is a white poster with a couple of toppled cows for a fake movie titled Cow-Tipping.
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.
Two arcade games and two pinball machines can be seen in the town's bar. One of the arcades is called the Mole Man, while the other one has an anthropomorphic evil cartoon lizard logo on it. The two pinball machines are Pool Shark, which has a cartoon shark logo on it, and what seems to spell Carlos, a seemingly western themed pinball. A character called D.P.O. from the episode of the same name holds the high score on one of the arcades in the bar.
When Scully enters the adult section of the VHS store, she comments that Mulder's XXX collection is bigger. Whn Mulder enters the adult sections he expresses his frustration over the fact that "Ass Lover 36" is out already.
Although the game is set during season 7 of X-Files and uses the same opening credits sequence from the first 7 seasons, Mulder and Scully's FBI badges, which can be seen in the items menu, are from the opening credits sequence of season 8.
On the password-protected computer in the asylum, Scully discovers a list of names including those of the missing girls. There are 17 other names next to theirs. Most of them are in-jokes. Addicott is audio programmer Neal Addicott, Barclay is the game's lead programmer Heather Barclay, Bouinatchov is animator Ivan Bouinatchov, Burneko is programmer Jesse Burneko, Cinelli is 2D artist Narry Cinelli, Cotton is senior 3D artist Jake Cotton, Field is art director Michael Field, Kleinberg is the game's designer and associate producer Seth Kleinberg, Kohout is the game's programmer and additional designer Rob Kohout, Lambert is the game's lead designer and producer Kirk Lambert, Langley is actually the game's lead animator Maggie Langley, Matson is the game's artist Eric Matson, Poon is 3D artist Heather Poon, Sanchez is animator Brian Sanchez, Turner is 3D artist David Turner, Ware is animator Sam Ware.
The optical storage reference sheet found by Scully during her search for the disk with data on Mulder in the Roush building contains Mulder's and four other names. These other four people are art director Michael Field, and 3D artists David Turner, Randy Mills, and Chris Barnes.
During the level in the Roush Tech building, Scully must enter Mulder's number to get the optical disk with his information. However, if she enters the number next to Chris Barnes' name she will receive extra health in the inventory infinite times. This Easter egg was added by one of the programmers as thanks to Chris for his helpfulness.