In 35,000 BC, two cavemen pursue an alien into an ice cave in the north Texas area and kill it, whereupon one is quickly infected by black oil that bleeds from the creature. In present day north Texas, a boy is infected with the oil after falling into a cavern and finding the cavemen bones. After an initial emergency response fails, a black helicopter arrives with people in biohazard suits to secure the area.
One week later, Mulder and Scully, having been reassigned but still part of the same team following the closure of the X-Files, are investigating a bomb threat to a federal building in Dallas. On a hunch, Mulder searches the building across the street and finds a bomb hidden in a vending machine. The building is successfully evacuated, but the bomb technician allows the device to explode, leveling a good portion of the structure. Mulder is surprised to hear that despite the building apparently being cleared, a young boy and three firefighters were found dead in the debris.
Mulder is also depressed when Scully tells him she is considering reassignment, and goes to a bar to drown his sorrows. There, he meets Dr. Alvin Kurtzweil, who says he used to work with Mulder's father and also that the Dallas building had a FEMA quarantine center that was destroyed to cover something. Back in Texas, Cancer Man arrives at some sort of well-guarded facility that has been set up at the cavern and is shown a parasitic alien that is growing inside a surviving firefighter. Cancer Man orders that he be kept alive so a vaccine can be tested.
The agents find that one of the Dallas bodies, being kept in the Bethesda Naval Hospital, is more disease-jellied than blown up. Someone pegs a child pornography charge on Kurtzweil, and he is driven into hiding. He tells Mulder how a plague is being manufactured to allow FEMA to come to power as a secret government. Yes, this movie was made well before Katrina.
The alien burrows out of the surviving firefighter and attacks a Syndicate doctor, who is left for dead. The Syndicate meets in London, and it is revealed that a virus has mutated into a new biological entity. The Well-Manicured Man is displeased, thinking it means their work towards colonization has been a lie. Mulder and Scully return to Texas to find that the operation has been completely removed, but are tipped off to the direction some unmarked tanker trucks went by the local kids. They happen upon an enormous cornfield and a couple of giant domes that release a swarm of bees, and narrowly escape pursuit by a pair of black helicopters.
Back in DC, Scully gets an order to transfer to Salt Lake City. The agents share a tender moment, which is rudely interrupted when a bee stings Scully and infects her with the alien virus. Mulder is shot and nearly killed by the fake paramedics who pick her up, and Scully is spirited away on a plane. The Syndicate does away with Kurtzweil, who has written a few books on the coming Armageddon. Mulder leaves the hospital unnoticed with help from The Lone Gunmen, and the Well-Manicured Man gives Mulder a weak vaccine against the virus and the coordinates for the Antarctic location where Scully is being held. He says the aliens placed the virus on the planet to infect its inhabitants at a later point, that the Syndicate has been trying to find a cure as a way of helping themselves, and that without a vaccination only alien-human hybrids will survive. He also says that Mulder's father gave up Samantha in the hopes that Mulder would uncover the project.
Mulder goes to Antarctica. The Well-Manicured Man, who has apparently killed himself with a car bomb after revealing the secrets to Mulder, has also hinted that the scope of the Syndicate's project is pretty big. Sure enough, Mulder finds thousands of cryogenic pods at a facility beneath the base. He finds Scully and administers the vaccine, which infects the whole system and starts to break it down. The Syndicate evacuates, and Mulder manages to escape with Scully as an enormous spacecraft exits the ice and flies off.
Of course, no one believes the agents. The tanker trucks are sent off with fresh labels, the corn fields are burned down, and only the bee that stung Scully is left as any sort of evidence. The Texas ordeal is covered up as a Hanta virus outbreak. Mulder urges Scully to go off and do her own thing so she doesn't have to be caught up in his crusade (and imprisoned in Antarctica and all that), but she vows to stay with him. In Tunisia, Cancer Man visits another corn-bee operation run by a Syndicate member and produces a telegram advising that the X-Files have been reopened.
Martin Landau, who plays Kurtzweil, is a fairly well-known actor, namely from his role as Rollin Hand in Mission Impossible. Ted King, who plays an FBI agent on the roof, also played Lorenzo Alcazar on General Hospital. And I'm a big Lost fan, so I guess I'll mention that Terry O'Quinn of John Locke fame briefly appears to get blown to smithereens.
Movie Body Count
Caveman-sicle: found encased in a glacier.
Two cavemen: one is killed by an alien, another is infected by the black oil. Even if he didn't die then, it was tens of thousands of years ago and he's not coming back.
35,000 BC alien: stabbed to death by a caveman.
Agent Darius Michaud: killed after he allows the vending machine bomb to go off.
Stevie and three firefighters: possibly killed by the black oil or other means; their bodies are found in the Dallas building after the explosion.
At least five Bethesda Naval Hospital bodies: nine bodies are visible in the morgue, and since one of them is one of the firefighters found in Dallas it's possible that three other bodies could be from the same site.
Another firefighter: left dead after an alien burrows out of his torso.
Dr. Ben Bronschweig: killed by said alien.
Dr. Alvin Kurtzweil: apparently killed by the Syndicate.
Well-Manicured Man's driver: shot by the Well-Manicured Man.
Well-Manicured Man: killed by a car bomb, apparently a suicide, after revealing a good deal of the Syndicate's work to Mulder.
Cumulative Body Count (117/202 episodes, 1/2 movies)
Humans: 1,432Creatures: 88
Grand Total: 1,581