When a religious cult operating in Canada unearths a spacecraft similar to the one Scully discovered in Africa, a plot is set in motion to kill baby William.
At the U.S./Canadian border in North Dakota, two night patrol agents spot a motorcyclist attempting an illegal border crossing. The agents give chase until the cyclist runs out of road and soars over a rocky ravine, his motorcycle bursting into flames.
Amidst the cyclists belongings are rubbings of symbols taken from an alien spacecraft. Later, Kersh and Follmer question Scully about the rubbings, but she refuses to cooperate until they reveal more about who or what is under investigation. She then makes her way to the X Files office, where she digs out a file containing the rubbing taken from the alien ship discovered in western Africa. She asks Reyes and Doggett for their help in solving the puzzle.
Doggett goes to the Canadian border, but discovers that the FBI cannot locate the cyclist�s body. In another wooded area nearby, the cyclist heals his injuries using an alien artefact.
Meanwhile, Scully meets with Reyes to discuss the alien rubbings, which seem to contain text from the Bible, the Koran and scripture from around the world, although the spacecraft predates all of those by millions of years. Scully suspects the writings contain secrets about baby William.
Skinner refuses to provide Doggett with information pertaining to the investigation, so he sneaks into Skinner�s office and steals a file and the alien rubbings. Meanwhile, an excavation team in Canada works on unearthing a buried spaceship.
Doggett makes his way to Reyes� apartment and shows her the information stolen from Skinner�s office. It turns out that the cyclist is Special Agent Robert Comer. Doggett and Reyes contact Scully and ask her to meet with them to discuss the findings.
It turns out that Comer infiltrated a UFO-worshiping religious cult based in North Dakota. The cult fled to Canada for reasons unknown to the agents. The FBI then concluded that Comer �turned to the dark side� and became just as crazy as the UFO worshipers he was investigating. Reyes then reveals that the rubbings Comer had in his possession do not match those of the craft found in Africa, so a second spacecraft must have been unearthed.
When Scully returns home, she discovers her mother on the floor, her face bloodied. Mrs Scully warns that someone is trying to kill the baby. Scully draws her weapon and races into the nursery. Comer overpowers Scully, throws her out of the nursery and slams the door shut. He then picks up a pillow and starts to put it over the baby. Scully bursts open the door and opens fire, shooting Comer three times.
Doggett and Reyes race to Scully�s apartment, where Comer lays dying. Despite Scully�s objections, Doggett calls for an ambulance. Before Comer loses consciousness, Comer tells her that baby William must die. Later, Scully finds the alien artefact amidst Comer�s possessions.
In Calgary, a woman in an overcoat reads about Comer�s shooting in a newspaper. She relays the news to the excavation area, where a Lone Man tells her, �there�s only one thing to do.�
Back at the FBI, Kersh and Follmer meet with Scully, Doggett and Skinner. Follmer explains that Comer was dispatched to infiltrate the cult based on a series of threats made on Mulder�s life. The FBI intercepted a message that Mulder was already dead.
Back at home, Scully enters her bedroom when she hears a strange sound. She notices the top drawer of her dresser bouncing violently. Scully opens the drawer, releasing the alien artefact, which flies across the room and into the nursery. It stops just above baby William�s face and he plucks it out of the air. Just as quickly, Scully snatches it back.
Scully packs a small suitcase and Reyes and Doggett follow her out of the apartment. On the street, Doggett spots the Overcoat Woman (from the excavation) sitting in an SUV. Reyes and Scully drive off, but Doggett remains behind. When Doggett approaches the SUV, the engine roars to life and heads toward him. Doggett draws his gun and fires a shot, but is run down.
Meanwhile, Scully and Reyes meet up with the Lone Gunmen, who promise to care for baby William. But as the Gunmen drive away, the Overcoat Woman pulls out a gun, and Langly loses control and crashes. When Scully and Reyes return to the apartment, they learn about Doggett. Scully realizes her baby is in jeopardy and heads off. Meanwhile, the Overcoat Woman places a gun to Byers� head, demanding the baby.
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