Revealing mistake: In the end when Mulder is reading the paper in the park. The paper is clearly a prop. Only the frontpage is real - when he puts the paper away you can see that the rest of the paper consists of blank pages. (01:45:45)
Scully is kidnapped after she's infected with the virus by one of the bees from the corn-field. Mulder is shot in the head and is apparently dead, but he soon recovers and recives the antivirus and the location where Scully is by the guy that killed Martin Landau. Soon after that, he's killed by a bomb in his car. After that, Mulder heads to Antartica (which is where Scully is)and discovers an alien facility where the ones that have been infected are held. Mulder gives Scully the antidote and infects the facility by doing it. Mulder and Scully try to escape from the facility which was actually a ship. The facility/ship leaves earth and Mulder and Scully survive and return to do what they do. After that the Cigarrette Man delivers a letter to a man, the letter said "X-Files re-opened". Then we see a closing shot of the same corn-field that Mulder and Scully saw... except that this one is in the Nairobi Desert.
Trivia: Early on in the film, just after Fox notices that the toilet in the bar is out of order and he goes outside - as he is relieving himself, he is facing a poster for Independence Day - another movie about alien invasion. Chris Carter, the producer of the X-Files, hated Independence Day and so had Mulder relieve himself nearby deliberately.
Question: If the "cold drink" vending machine was unplugged and the buttons were unresponsive, WHY did the saboteurs deliberately illuminate the front of the machine? Wouldn't this ATTRACT people to the machine, only to subsequently arouse curiosity when it failed to function (as it did with Mulder)? The more logical approach would be to disable the vending machine (including the illumination) and tape an "out of order" sign on it. People would then just ignore the machine, arousing no suspicion. The illuminated vending machine gimmick looks like an illogical contrivance to advance the plot.
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