In Blackwood, Texas, a boy, Stevie, falls through ground near his home into an underground cave.
     Black Oil flows out of the ground and enters his body. Three friends call for help, and the Black Oil
     also enters three firemen who enter the cave to rescue Stevie. A mysterious bio-containment team
     arrives and hauls off the four infected people.

     With the X-Files closed, Mulder and Scully (still partners) are in Dallas to assist with the search for a
     bomb. A threat has been received to blow up the Dallas Federal building. They are in a nearby building,
     checking it for explosives, because none have been found in the Federal building. Taking a break from
     the search, Mulder enters a room with vending machines and discovers the bomb inside a vending
     machine, but he is locked in the room. Using cell phones, he informs Scully who mobilizes authorities
     to evacuate the building. A cutting torch is used to open the door to the vending room. The agent in
     charge orders everyone else out of the building, indicating that he will disarm the bomb alone. We see
     that he takes no such steps, and a massive explosion rocks the building, as the final evacuation
     vehicles race away from the scene.

     Back in Washington, Scully testifies before an investigation committee that, in effect, is looking to
     place the blame for not preventing the explosion. Scully and Mulder learn that a boy and three firemen
     have been reported killed in the explosion. Scully is informed that she and Mulder will be split up, and
     she considers resigning from the FBI. Later, Mulder goes to a bar to drown his sorrows, and meets
     Dr. Kurtzweil, who says he was an associate of Mulder's father, but who left the Project. Kurtzweil
     claims that the four fatalities in the explosion were already dead before the explosion, in a Federal
     Emergency Management Agency office in the building, and that the explosion was to cover their
     deaths.

     We see a scene at the bio-containment facility set up at the cave. Another human body is there with its
     skin turning transparent. Inside a creature can be seen, growing and feeding on the body as scientists
     study it. The alien unexpectedly exits the body, before the vaccine can be tested. It attacks one of the
     scientists.

     The Elders meet in London and are alarmed that the virus has mutated. Instead of just occupying the
     human body, it is growing a new alien organism inside. They decide they must present this
     information to the Colonists by giving them a human body in which an organism is growing. (The
     movie is unclear, but Chris Carter's comments on the X-Files CD suggest that the Virus/Black Oil
     and the Colonists may be different factions of aliens, and that the Bounty Hunters are half-humans,
     engineered by the Consortium to be immune to the virus.) During this meeting we meet Strugholdt,
     who is the apparent leader of the Consortium. He lives in Africa and flew in especially for this crisis
     meeting. 

     Mulder rousts Scully out of bed and they go to a Washington morgue where the bodies of the four
     fatalities have been sent. She finds that they were not killed by the explosion but have some sort of
     virus in them that is disolving their internal organs. The agents fly to Texas and find evidence of the
     same virus in archeological bone fragments recovered from the explosion -- apparently the remains of
     one of the hunters 35,000 years ago. The local officials tell Mulder and Scully where the bones were
     collected and they go there, to the site where Stevie fell into the cave. Stevie's friends tell the agents
     that the trucks just left an hour earlier, and the agents pursue. They eventually find a field of
     irrigated corn in the middle of the Texas brush. At night they enter one of two illuminated domes in
     the field. As they are exploring, louvers open releasing swarms of bees. As Mulder and Scully run,
     they are chased through the corn by helicopters.

     Back in Washington, Scully presents her additional evidence to the investigation committee, but they
     are unconvinved. At Mulder's apartment later, she tells him that she has been transfered to Salt Lake
     City, but that she has resigned. Mulder entreats her to continue to help him pursue the truth. In a
     tender moment they almost kiss, but Scully is stung by a bee that has apparently been inside her
     clothing all the way back from Texas. She immediately goes into shock. Mulder calls for help and an
     ambulance quickly arrives. At the last minute as they depart with Scully, the ambulance driver shoots
     Mulder. He wakes up in a hospital, under guard. The Lone Gunmen and Skinner help him leave
     secretly (wearing Byer's clothes with byers in Mulder's bed, talking with Skinner), and Mulder seeks
     out Dr. Kurtsweil at the bar. Instead he meets the Well Manicured Man. Kurtzweil is dead but the
     WMM (who opposes surrendering to the Colonists) invites Mulder into his car. He explains the alien
     virus, saying that it was the first live on Earth, millions of years ago. He says many aliens await
     underground to be revived when the Colonists arrive. He says the Consortium cooperated initially
     because they thought the human race would just be "occupied" by the virus (also known as the Black
     Oil). It has become apparent, however, that the Colonists plan to use humans to gestate a new race of
     aliens, which is a violation of their aggrement. The bees distribute the alien virus that is picked up
     from geneticly engineered corn pollen. WMM gives Mulder a vaccine and geographic coordinates
     where Scully can be found. WMM dies in an explosion of his car just after Mulder leaves, because he
     betrayed the Consortium.

     Mulder makes his way to Antartica 48 hours later, and on a borrowed Snowcat he discovers an
     installation where WMM said it would be. As he approaches, he falls into a hole in the snow, sliding
     several dozen feet or more down a pipe in the snow. He finds himself inside a huge alien spacecraft. He
     eventually finds Scully, naked and sealed in a fluid canister that is apparently used to incubate the
     virus inside her. He breaks the canister open and injects her with the vaccine. There is a quick
     response that also affects the hundreds or thousands of other conisters, also containing incubating
     humans. He somehow finds clothing for the semi-conscious Scully and helps her out of the spacecraft.
     At one point he has to perform CPR on her. At another they are pursued by the same highly
     aggressive aliens, saved only by an earthquake caused by the ship beginning to move, that knocks the
     aliens back down into a hole in the ice. As Mulder and Scully run away from the site of the ship, the
     ice and snow collapses behind them, forming a giant crater that expands behind them as they run.
     They barely escape as the giant ship lifts off and departs. Scully is groggy and does not see the ship
     depart.

     Again returning to Washington, Scully presents her final evidence to the investigation committee.
     Her conclusion is that the FBI does not have an investigation unit competant to study the evidence. In
     the Tunesian desert, we see another field of irrigated corn, and the domes housing the bees.
     Strugholdt and CSM talk and CSM receives a telegram saying "X-Files reopened, please advise."

     In Washington, Mulder tells Scully that she was right to quit, but she says now that she cannot,
     because that way "they" would win. The movie ends with the X-Files reactivated and the agents ready
     for new challenges.