S8E4 · Roadrunners

In the desert near Sugarville, Utah, a hitchhiker catches a ride from a passing bus, which soon stops without explanation. The hitchhiker watches a man with crutches leave the bus, joined by the other passengers. Following them, he sees them stone the man to death. They later surround the hitchhiker as he tries in vain to escape.

FBI special agent Dana Scully (Gillian Anderson) goes to investigate the murder. The victim, a twenty-two-year-old backpacker, now shows signs of body decay usually associated with old age. Later, at a pay phone, she asks her partner, John Doggett (Robert Patrick), to check the X-Files for cases mentioning glycoproteins. While discussing the case with Doggett, the bus passes her, and she follows it to a gas station in the middle of the desert. A man with an injured hand learns that she is a medical doctor and fills her car with gasoline laced with water. After her car stalls, Scully returns to the gas station and is told that rain got into the gas canister.

The attendant tells Scully that Mr. Milsap is the only person with a working phone, but she discovers that the line is dead. Mr. Milsap offers Scully a room at the local boarding house, but Scully tries the rest of the town only to be ignored by everyone; they are all too engrossed in Bible -study groups. Disturbed by the turn of events, she keeps her gun close at hand. The next morning, Mr. Milsap tells Scully that there is a man who needs help downstairs. She goes with him and finds the hitchhiker from the episode's opening scene having a seizure.

She advises them to take him to the hospital, but they claim that they do not have any cars. While examining the man, Scully discovers a strange, circular wound on his back. Meanwhile, Doggett calls the sheriff at Scully's original destination and learns that Scully has not yet arrived and he sets out to find her.

The sick man begins to recover, and Scully talks to him while the townspeople are gone. He does not seem to know who he is or how he arrived. She inspects his wound again and finds a lump moving along the man's spine; digging into the open wound, she pulls out a piece of a large worm. Scully talks with the hitchhiker, Hank, about the creature and believes she cannot get it out without killing him. Scully goes to find a car but, moments after leaving, Hank immediately tells the townspeople what she is up to and that "another swap" is needed. Concurrently, Doggett arrives in Utah and informs the Sheriff about a series of X-Files involving similar back wounds and death by stoning.

Scully is eventually captured by the townspeople and the worm is inserted into her body. She is tied to a bed and told by the people what an honor this is. When Doggett arrives she tries to alert him but is gagged before she can do so. Eventually, Doggett finds Scully, cuts the worm out of her, and shoots the creature dead. Later, Scully is packing her things in the hospital when Doggett comes in to inform her about the trial of the cult members; they are offering little defense except that they claim that they are being persecuted for their religious beliefs. Scully muses that they thought the worm was the Second Coming of Jesus Christ. She apologizes to Doggett for going out on the mission alone and promises never to do so again.