- The final scene takes place in Foum Tatouine, which is an actual place, used for filming the scenes on the planet Tatooine in Star Wars (1977) and Star Wars: Episode VI - Return of the Jedi (1983).
- In the original trailer, the shot with Mulder & Scully running from the bees was used, albeit minus the SFX bees.
- After consuming much alcohol and finding the bar's bathroom locked, Mulder relieves himself on a movie poster for Independence Day (1996). A line in Independence Day, spoken just after the first shot of the cable station, is "Yeah, I love X-Files too. I hardly get to see it."
- Conrad Strughold (Armin Mueller-Stahl) was named for the real Strughold, a Nazi scientist who conducted experiments on prisoners during World War II.
- Former LAPD bomb squad officer Herb Williams and former FBI agent William O. Heaton acted as advisors for the bomb sequence - and appeared in the movie as agents in a scene with Scully.
- The newspaper article Mulder reads at the end of the film (titled "Fatal Hanta Virus Outbreak in Northern Texas Reported Contained") was written by reporter Howard Dimsdale. The real Howard Dimsdale taught X-Files writers Frank Spotnitz and John Shiban at the American Film Institute, and was blacklisted during the McCarthy era, when he wrote under the name Arthur Dales, which was used as a name for the characters played in the series by Darren McGavin, M. Emmet Walsh and Fredric Lehne.
- 619 - the number on the "Office of Professional Review" door (where Scully is interrogated by the Assistant Directors). 06/19 is the date that the movie opened.
- 11:21 - the time Mulder goes to the Dallas Field Office, where Scully joins him and analyses the fossils. 11/21 is the birthdate of Chris Carter's wife.
- Ten Thirteen Productions produced the film and the television series. On the last track of the movie soundtrack, if you let it play until 10:13, Chris Carter gives a description of some of the various conspiracies in the series and the movie. 10/13 is also the date in which the film came onto VHS in 1998.
- In the chronology of the series, the movie takes place between the fifth season finale, episode #5.20 "The End" (with the CSM torching Mulder's office) and the sixth season premiere episode #6.1 "The Beginning" (which deals with the gestating-breed of aliens in the movie).
- The scene in which Scully and Mulder are chased through a cornfield by helicopters is a reference to the famous "crop duster" scene in North by Northwest (1959). Martin Landau was in both movies.
- As is the case with many 20th Century Fox Films, the film cans for the advance screening prints and show prints had a code name. The The X Files (1998) was "Nuts and Bolts."
- The working title "Blackwood" came from the works of English writer Algernon Blackwood (1869-1951), a member of the Golden Dawn Society, about a race of intelligent beings who predated humans. The fire trucks arriving to rescue Stevie (Lucas Black ) have "Blackwood County" printed on the doors
- Stevie (Lucas Black) is named after one of the original series creator Chris Carter's boyhood friends. Carter says that he and the real Stevie used to dig holes a lot, just like in the movie.
- Watch the scene where the agent's car (chasing the white trucks) is tracked by a helicopter shot driving bottom right to top left diagonally across the screen. This scene cross-fades into the end of the drive at night, with the car driving top right to bottom left diagonally. The cross fade between the two shots creates a huge "X" on screen for a moment or two.
- Foum Tatouine is actually filmed in California according to the commentary track.
- At the end of the scene with the chasing of the white trucks, Moulder and Scully have a talk. The cuts showing Moulder talking by the roadside had lights in the background that needed to be removed in post production. 24 frames per second, at about $1000 per frame. Director Chris Carter on the commentary admits this $25k/second mistake in filming.
>>> WARNING: Here Be Spoilers <<<
Trivia items below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- SPOILER: Terry O'Quinn, who plays Darius Machaud, dies in the bomb sequence at the beginning of the movie, yet returns in Season 9 as the Shadow Man in "The X Files: Trust No 1 (#9.6)" (2002) - only to die again in the Magnatite quarry.
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