Hank Gulatarski waits for what seems like hours at a Roadrunners bus stop on a deserted road in Juab County, Utah. The faint rumble of a bus in the night stirs him, but it nearly passes him until he flags it down. The unmarked bus stops and he walks on, past the passengers who eye him suspiciously. Their silence puts him off a little, but he plops down in a seat and shuts his eyes. All of a sudden, the bus stops and the people file out in an orderly fashion. Confused, Hank follows them. The Bus Driver and the other passengers begin to bash a disabled man's skull with rocks. They turn and approach Hank, who yells as they swarm over him.

Days later, Scully collects evidence from the desert crime scene. She calls Doggett from a pay phone to say that she is consulting on a murder case where a traveler with a deteriorated body was beaten to death. She asks Doggett for help in tracking down an old X-file that mentions mucus. Although Doggett is somewhat put off about being left behind, he agrees to do her research. Scully pulls into an almost abandoned filling station for some gas. The pumps are empty, but when she mentions that she is a doctor, the Gas Station Man kindly fills her tank with a reserve in a can. After Scully pulls away, the Gas Station Man walks into the nearby boarding house where the Bus Driver is tending to the ailing Hank. "Help is coming," he says. Further on up the road, Scully's car putters to a halt. She walks back to the gas station to find the can of gas was really full of water. The Attendant sends her to the boarding house to use their phone. There, Mr. Milsap greets Scully by telling her his phone is out of order. He offers her a room for rent, but she is dubious of his intentions. She storms outside, unconsciously touching her stomach as if trying to protect her unborn child. She sees a woman who ignores her calls and Scully notices people inside the houses holding religious services. With no other option, Scully takes Milsap's room for the night. She waits in her bed with her gun cocked at the ready. Back in Washington, Agent Doggett calls the local Juab sheriff's office, but Scully has not turned up there. He asks the local police to send out a cruiser to look for her.

The next morning, Milsap asks her medical help for another man. Scully finds Hank shaking with grand mal seizures and she notices a wound on his lower back that is bleeding badly. Thinking he is maybe diabetic, Scully tries to raise Hank's blood sugar, but this does not work. The Bus Driver sobs. Suddenly, Hank awakens and asks to speak with Scully privately. He doesn't remember who he is or how he got there. She tells him about the murder in the area and her suspicion of the townspeople to be part of a cult. When she tries to lift him, Scully finds that the hole in his back has something moving under his skin. She uses tweezers to pull out a part of a slug, but the remainder of the creature crawls over his spine. Suspecting that the people put the slug inside him, she fears for Hank's life. Leaving Hank her gun, she escapes through a window to find a car. Milsap and the Bus Driver enter Hank's room. Hank recounts Scully's diagnosis that he is dying. He tells them that they need another swap.

Doggett discovers that Scully's phone call was made from a payphone that Hank had used before his disappearance. Doggett goes to Utah with case files about others killed by stoning with the same wounds on their lower backs. Scully finds the bus inside a shed, but doesn't notice the townspeople following her. They surround her. Hank bends over and the others stone him, all the while shouting "Amen!" They remove the giant slug from his body and approach Scully. She screams for mercy, exclaiming that she's pregnant. They lift her shirt and bring the creature to the small of her back. After it enters her body, they return to the boarding house and tie her to a bed. Milsap softly says that she will soon be one with Him. A light shines through the window as Doggett pulls up in a car. Milsap and the Bus Driver greet him, but say that they haven't seen Scully. Scully manages to kick a gas lamp off the table to start a fire and the Gas Station Man kicks out the flame, but Doggett doesn't notice.

Doggett radios the sheriff, suspicious of the people, and goes back to the boarding house. He finds Scully, unties her and carries her to the bus. She screams in pain, begging Doggett to cut out the creature climbing up her spine. The townspeople find them and attack the locked bus. Doggett yanks the slug out of Scully's neck, throws it on the floor and shoots it. The mob quiets down and stares at the obliterated creature. Milsap asks "Why?" The people begin to cry. Doggett carries Scully out of the shed, as a hoard of police cars raid the building.

One week later, Scully packs her bag in a Salt Lake City hospital. Doggett tells her that all of the forty-seven cult members are sticking together in the face of a grand jury hearing. They believe that the creature was the Second Coming of Christ. Scully apologizes for leaving him out of the case, citing that it was nearly a fatal mistake. She promises not to do it again.