The X-Files movie begins a long, long time ago, in 35,000 b.c., when much of the earth was covered in ice and snow. Two figures, primitive men, walk through the cold, windswept landscape. They are following the trail left by a mysterious creature. Three-toed tracks lead the hunters to the inside of an ice cave. The creature is an alien--tall and thin, black-eyed and hairless, with only tiny slits for a nose and mouth. But the alien has razor-sharp teeth and long claws on his hands and feet that extend when it attacks. Suddenly the alien lashes out and fiercely attacks one of the men. One dies in the battle. The second primitive struggles and finally kills the alien. But then we see a scary black oil ooze out of the dead alien's body. It seeps into cracks on the floor and wall. The black oil seems to be alive! It creeps slowly toward the surviving primitive's chest, mouth, and eyes. Without warning, a boy plunges through the roof of the cave. The movie has cut to the present, to Blackwood, Texas, an area outside of Dallas. A group of boys have been playing at the same cave we saw in the first scene. But now, thirty-five thousand years later, the ice and snow have melted away. Instead, the cave is rocky, and in the middle of empty desert land. The boys, trying to build a fort, have dug a hole in the hard desert ground right above the cave. One of the boys--Stevie (Lucas Black)--digs too deep and suddenly falls through a hole in the earth. He falls so hard the wind is knocked out of him, but he is okay. Exploring the cave, Stevie discovers a human skull and excitedly tells his friends there are lots of bones in the cave. Suddenly, from a crack in the cave floor comes the same gooey, black substance that seeped into the floor thirty-five thousand years earlier. The black oil slowly inches toward the boy. It creeps onto his shoe, crawls under his skin, and moves through his body until even hhh his eyes turn black and oily. Terrified by what has just happened to their friend, the boys run for help. Stevie stands frozen within the cave. The creeping alien oil has paralyzed him. Suddenly the air is filled with sirens. Soon, there are fire trucks everywhere. Two firemen quickly climb down into the cave to rescue Stevie. Mysteriously, they don't come back. Two more firemen are sent in--and disappear, too. The bodies of all four men have been invaded and infected by the alien oil. The local fire captain is concerned when no one returns from the cave. Now the fire department has to rescue five people instead of one. Just then, a helicopter swoops down for a landing. Dr. Ben Bronschweig (Jeffrey DeMunn) gets out. He has brought along a mysterious "hazardous materials" team. The team has seen dangerous substances like the black oil before. They carefully and quickly carry Stevie's paralyzed body away. The rest of his team begin setting up tents and other equipment at the site. What the local firefighters do not know is that Dr. Bronschweig reports to a secret organization known as "the syndicate." This cave has become an important part of the undercover "project" the syndicate is working on. Dr. Bronschweig will set up a laboratory here to observe one of the infected firemen. The movie action cuts to a government building one week later. Someone has planted a bomb here. FBI agents must hurry to find the bomb before it goes off. The FBI has cleared out all of the people who work there, and is now looking for where the bomb is hidden. But two agents have decided to check the building across the street instead. One of them, Fox Mulder (David Duchovny), a handsome man with sad eyes and a quick sense of humor, has a hunch that the FBI is on the wrong track. His longtime partner, Dana Scully (Gillian Anderson), a beautiful red-haired woman, is on the roof of the building, but she speaks to him by cell phone. Together they used to be in charge of the FBI's X-Files unit. But now, that unit has been closed. In the X-Files unit they investigated, or looked into, events that were strange or difficult to explain. Now they are assigned to more common FBI duties--like checking out bomb threats. Mulder's hunch is right. By accident, he discovers the bomb hidden in a soda machine in the building across the street. With Mulder locked in the vending room, Scully hurries to clear the building. She calls for help from the FBI agents next door. With just minutes to spare, Mulder is rescued by Scully and Special Agent in Charge Darius Michaud (Terry O'Quinn). Michaud orders Mulder and Scully and everyone else out of the building while he stays behind to try to defuse the bomb. As the car speeds away, the bomb goes off. The building explodes in a shower of cement, metal, and broken glass. The next day Mulder and Scully are at FBI headquarters in Washington, D.C., where they are questioned by Assistant Director Jana Cassidy (Blythe Danner). She wants to know everything they saw and heard before the bombing in Dallas. The agents learn that five people were killed in the explosion. Special Agent in Charge Michaud, three firemen, and the young boy, Stevie, all died in the blast. Mulder and Scully also learn that they are being blamed for those deaths. That night, Mulder meets Dr. Alvin Kurtzweil (Martin Landau). The doctor claims to be an old friend of Mulder's father. He also writes books about government conspiracies--plots to hide information or evidence from the public. Kurtzweil gives Mulder important news. The building in Dallas was bombed by the syndicate to hide the already dead bodies of Stevie and the three firemen. The syndicate did not want anyone to find the bodies, so they blew up the building. Kurtzweil also tells Mulder that Special Agent in Charge Michaud let the building explode because he worked for the syndicate. Mulder is disturbed by what Kurtzweil has told him. He talks Scully into going to the naval hospital where the bodies are being kept. At the hospital, they go straight to the cold, dark morgue--a place where dead bodies are temporarily stored. Since Scully was trained as a doctor, she carefully examines the body of one of the bombing victims. She snaps on her medical gloves and does an autopsy--or exam--on one of the firemen. Scully quickly discovers the fireman did not die from the explosion, as someone wanted the agents to believe. He died from some kind of infection. It is one she has never seen before. The victim's skin is almost see-through and feels like sticky gelatin. His internal organs--like his heart, liver, and kidneys--have been partially eaten away by the virus. While Scully examines the body, Mulder meets with Kurtzweil again. The doctor warns Mulder that the syndicate is involved in a secret government "project" to deliberately release a terrible plague. He says the syndicate has been working on the project for over fifty years! But Kurtzweil can't or won't give Mulder any proof--he tells him to go to Dallas to search for the truth. With this new information, Mulder asks Scully to meet him at the FBI field office in Dallas, Texas. There they look at the scattered waste from the bombed building. The two agents are shown ancient pieces of bone called fossils which were found at the bomb site. The FBI field agent tells them the fossils had originally been found at an archaeological dig site and had been kept in an office in the building that exploded. Scully looks at the bone fossils under a microscope. The same virus that killed the fireman is also in the fossils. Back at the cave site, the Cigarette-Smoking Man (William B. Davis) arrives in a black helicopter to talk to Dr. Bronschweig. Dr. Bronschweig's team has set up a high-tech lab at the site, and it is very cold inside. The doctor explains that they have lowered the temperature to freezing to slow the development of the virus. They view the body of one of the firemen, who is barely still alive. His skin is gray and gelatinous, like the bodies Scully saw at the hospital, and there seems to be something alive inside him. Something that blinks. The virus has mutated into a living organism! Dr. Bronschweig asks the Cigarette-Smoking Man if they should destroy the body before the new organism grows any larger. "No," answers the Cigarette-Smoking Man, "we need to try our vaccine on it." After the Cigarette-Smoking Man leaves, Dr. Bronschweig returns to the cave to administer the vaccine, only to find the infected fireman's chest ripped wide open. The organism that was growing inside of him is gone. Seconds later, the fully grown alien savagely attacks the doctor with his sharp claws. Dr. Bronschweig calls for help, but the crew, worried that he is now infected, quickly fills the cave hole with dirt so the creature cannot get away. They bury Bronschweig and the alien forever. When Mulder and Scully go to the cave site to investigate, all they see is a brand-new playground. They question Stevie's playmates, and learn that tanker trucks left the playground just minutes earlier. The two agents speed away to see if they can find the trucks. They drive for hours without seeing anything until they finally reach a dead end at a railroad crossing. Just when Mulder and Scully are about to give up, a train comes by carrying the tanker trucks. The agents follow the train until it stops at a cornfield. Mulder and Scully are confused about what a cornfield would be doing in the middle of the desert. There are several strange, giant, white domes in the middle of the cornfield. They enter one of the white domes, but are suddenly chased out by swarms of bees. When they get outside, mysterious, low-flying helicopters chase them through the cornfield. Mulder and Scully make it back to Washington, D.C. Although Scully does not know it, one of the bees is hiding in her jacket. Scully tells Assistant Director Cassidy that she and Mulder went back to Dallas and discovered evidence that the bombing was a cover-up. Later Scully goes to Mulder's apartment to tell him she is going to quit the FBI because she has been assigned to another city. Mulder and Scully have worked together for a long time and have developed a close friendship and deep respect for each other. Mulder asks her not to quit. He doesn't know if he can continue on without her. Just then, the bee hiding in Scully's jacket stings her and she falls to the floor in Mulder's hallway. Mulder calls an ambulance and a uniformed medical team comes to take Scully away. But they are not real ambulance drivers. When Mulder asks which hospital they will be taking Scully to, the driver shoots Mulder. He is wounded in the head. As the ambulance pulls away the real ambulance pulls up and sees Mulder lying on the ground. Later, Scully's unconscious body is put into a cryolitter--a kind of clear refrigerated box. It is loaded onto a plane at the airport, headed for the Antarctic. Mulder wakes up in a Washington hospital. Luckily, he is not badly hurt. His friends the Lone Gunmen (Bruce Harwood, Dean Haglund, and Tom Braidwood) are there. The Lone Gunmen have helped Mulder in the past. They tell Mulder someone listened to his phone call and sent a fake ambulance. Mulder asks the Lone Gunmen to help him escape from the hospital. He knows he has got to find Scully. He arranges to meet Kurtzweil, hoping the doctor can tell him where Scully is. When Mulder arrives at the meeting place, he doesn't find Kurtzweil. Instead Mulder runs into the Well-Manicured Man (John Neville), who is involved with the syndicate. He gives Mulder Scully's location, as well as the vaccine that can save her life, but only if it is given to her in the next ninety-six hours. He also tells Mulder that the virus is extraterrestrial. The shadowy syndicate has been working with the aliens. But the syndicate has also been secretly developing the vaccine to protect the members and their families from the virus. Mulder doesn't know if he should trust the Well-Manicured Man. He thinks the Well-Manicured Man has killed Kurtzweil and put his body in the trunk of his car! The Well-Manicured Man drops Mulder off and tells him to go find Scully because only her science can save them. As soon as the Well-Manicured Man gets back in his car, it bursts into flames. The Well-Manicured Man is dead and Mulder runs off, realizing that time is running out. Next, the movie cuts to a snow tractor in Antarctica. We see Mulder, searching for Scully over the cold, grim land. He finds an ice station and, through binoculars, sees the Cigarette-Smoking Man leaving. As Mulder gets close to the station on foot, he suddenly plunges through the ice and tumbles down a deep ice shaft. He lands on what seems like a hard metal object covered with snow and ice. He lowers himself through a steam vent and crawls through the cramped passageway. It finally widens to become a huge and strange indoor space. Mulder doesn't know it yet, but he has stumbled into an alien spaceship, hidden beneath the ice. Climbing down to the hallways below, Mulder spots Scully in one of the thousands of cryopods--iced units in which bodies infected by the virus are kept. These bodies--called "hosts" because they host the virus so it can grow--are in a frozen state, but alive. Mulder breaks through the icy covering of the pod. He shoots the vaccine into Scully's shoulder with a needle. In moments, Scully begins to awaken. The tube in her mouth shrivels up and Mulder pulls it out so she can breathe. Suddenly the whole ship shudders and rumbles. The vaccine has woken up the ship, too. The inside of the ship begins to warm up. The heat makes the icy cryopod coverings melt. The aliens begin to wriggle around inside the host bodies. Mulder carries Scully back to the top of the ship. Scully stops breathing. While Mulder gives her CPR, the aliens begin to hatch from the bodies and break free of the cryopods. Scully regains consciousness just in time to escape the aliens. With one of the creatures not far behind, Mulder gets Scully to the top of the ship. They are out just in time, but the whole ice field is shaking and collapsing beneath their feet. Under the ice, the ship begins to rise. Mulder and Scully run for their lives, just a few feet ahead of the collapsing ice. Suddenly, they fall into a hole. Moments later, they land on what appears to be a section of the rising spaceship! The agents fall off the ship and land on the icy ground. Scully lies unconscious as Mulder watches the eerie ship rise higher and higher, until it is surrounded by swirling clouds and disappears into the sky. Back in Washington, Scully meets with Assistant Director Cassidy and other FBI officials. They question her about her report, in which she tells the story of what happened to her and Mulder. Assistant Director Cassidy thinks the report is too unbelievable to be true. Besides, there is no evidence to prove anything in Scully's report. Scully hands Cassidy a vial containing a dead bumblebee, the only evidence left. Later we see Mulder reading the newspaper. He sees a story about a virus outbreak in Texas, and he knows it is a cover-up. Scully comes over and he shows her the story. Mulder is frustrated and angry, but Scully is more hopeful. She has told the officials everything that happened. Mulder tells her that she should give up his hopeless cause, but she says if they quit now the bad guys will have won. The last scene takes place in Tunisia. We see a man walking along rows and rows of corn. It is the Cigarette-Smoking Man. He has come to talk with Conrad Strughold (Armin Mueller-Stahl), another member of the syndicate. The Cigarette-Smoking Man tells Strughold that Mulder is still on the case. Strughold tells him not to worry. One man alone cannot fight the future. "Yesterday," says the Cigarette-Smoking Man, "I received this." He hands Strughold a telegram which reads: X-Files re-opened. Stop. Please advise. Stop. Strughold sighs and drops the telegram, and walks back into the massive cornfield.