Chris Carter originally wanted to end the television series after the fifth season, and continue the show mythology with a series of films, beginning with this one. The Fox Network, however, saw the series as too profitable, and forced Carter to write this film as a tie-in between two seasons of the show, a task which he found very daunting.
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 hope I get to see it." However, the feeling wasn't mutual: Chris Carter loathed ID4 and had Mulder piss all over the film's poster to express his disdain for it.
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).
Shot in 10 weeks during the hiatus between seasons 4 and 5 of the show. Reshoots were also undertaken during production of season 5, which is why either Mulder or Scully are featured less prominently in some of the episodes which were made that year.
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.
At the end of the scene with the chasing of the white trucks, Mulder and Scully have a talk. The cuts showing Mulder 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.
Chris Carter's birthday is October 13th, i.e. 10/13. His production company, Ten Thirteen Productions, produced the film and the television series. On the original release of the movie soundtrack, the last song contains a hidden track beginning at 10:13 featuring Chris Carter giving descriptions of various conspiracies in the series and the movie. 10/13 is also the date the film was released on VHS in 1998.
Because the tagline "Fight the Future" was placed just below the title on the release poster, many X-Files fans took it to be a subtitle. It is still used among fans as an unofficial "episode title," rather than call it "the movie."
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.
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.
11:21 - the time Mulder goes to the Dallas Field Office, where Scully joins him and analyzes the fossils. 11:21 is also the time when Scully wakes up to Mulder calling her in The Pilot Episode and The Erlenmeyer Flask in the series. 11/21 is the birth date of Chris Carter's wife. Also, D-1121 is shown on one of the domes during the Antarctic section at the end of the movie. The D represents his wife's name, which is Dori.
The desert area with Dallas in the distance isn't real. A composite shot was used to make the effect. The Dallas area is actually very green and hilly, as is most of north Texas. These scenes were filmed in the high desert north of Los Angeles.
At 32min 20secs the "Cigarette Smoking Man" gets out of a helicopter, and proceeds to light a cigarette whilst still in the down wash of the rotor. He uses a lighter that sounds just like a classic Zippo lighter (known for being still able to work in extreme wind conditions).
At one point, Martin Landau's character is dismissively referred to as, "a Chriswell". This is a reference to the phony psychic / UFO prognosticator Criswell, who, among other things, was hired to play the narrator for Plan 9 from Outer Space (1959).
The trivia items below may give away important plot points.
This is the second time in which David Duchovny and Gillian Anderson kiss in the lips in outtakes. Both of them in a hallway, what contributed to make the hallways mythological places in The X Files. The first time was in Memento Mori, and the kiss was deleted because the producters didn't want that Mulder and Scully kissed for the first time because she had Cancer. In this occasion, Duchovny and Anderson kiss at least twice. In one of them Gillian Anderson crashes Duchovny into the wall and in the other he dissapears taking her away.
Terry O'Quinn, who plays SAC 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 (2002) - only to die again in the Magnatite quarry. He also played Lt. Brian Tillman in The X-Files: Aubrey (1995)