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.
Gillian Anderson's least favorite aspect of the shoot was the sequence where Mulder and Scully are running through a field of corn stalks. As she was running behind the much taller David Duchovny, she kept getting smacked in the face by the leaves.
After consuming much alcohol and finding the bar's bathroom locked, Mulder relieves himself on a movie poster for Independence Day : Le Jour de la riposte (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.
Getting a bee to walk along Gillian Anderson's shoulder was achieved by putting some pheromone in the air and gently blowing it with little fans in the direction they wanted the bee to move.
Glenne Headly was a huge fan of the show and readily accepted the tiny role of a bartender just to be involved.