The agents travel to Pennsylvania to investigate the mysterious death of Reverend Finley, a self-proclaimed Stigmatic whose palms suddenly bled as his rapt congregation looked on in awe. Mulder recalls a series of international, religiously-motivated murders in which the victims were all false Stigmatics like Reverend Finley. Scully notes ligature marks on Finley's neck, suggesting strangulation.

Meanwhile, in Loveland, Ohio, fifth grade student Kevin Kryder begins bleeding at the palms. His teacher, Mrs. Tynes, and fellow classmates look on in horror. The agents are informed by Carina Maywald, a Social Services worker, that Kevin's father, Michael, was institutionalized after he proclaimed the boy was the son of God. Mulder theorizes that Kevin may have inflicted the wounds on himself in protest over his father's incarceration. Now, Mulder fears the boy may become a target for the Stigmata killer.

At the mental institution, Michael Kryder professes his belief that "Forces of Darkness" are out to eliminate his son and thereby trigger Armageddon. He also believes that God will chose someone to protect Kevin and avert catastrophe. Surprisingly, Scully places more faith in the story than does Mulder.

Kevin is kidnapped from a social services dormitory by a bald, frightening-looking man. Based on a description from children at the dormitory, Mrs. Kryder identifies the man as Owen Jarvis, a gardener. The agents storm Jarvis' home and take him into custody. Kevin has run off. Owen claims God told him to protect the boy. Using great strength, Owen breaks his handcuffs and runs to the Kryder home. He finds the Millennium Man (the same man who murdered Reverend Finley) preparing to murder Kevin. A fight ensues, and the Millennium Man kills Owen. The agents arrive at the scene and rescue Kevin, but the Millennium Man escapes.

The agents trace finger prints burned into Owen's neck to Simon Gates (the Millennium Man), the owner of a recycling plant. Records indicate Gates visited Israel, and Mulder speculates that Gates may be suffering from the Jerusalem Syndrome, a condition that causes people to suffer religious delusions induced by the journey.

Susan Kryder and her son become stranded on a remote road after their car breaks down. Gates appears at the scene and chases after Kevin. Susan climbs into Gates' car and attempts to run him down. She loses control of the vehicle and dies in a crash.

The agents take Kevin to a nearby motel and place him under surveillance. As Kevin is taking a bath, Scully tells Mulder how his disbelief towards religious miracles is difficult to fathom given his open-mindedness towards the paranormal. Suddenly, a loud noise erupts from the bathroom. When the agents enter, they find Kevin has been abducted.

Scully notices a circular recycling logo on a trash bin. Suspecting she might be the person chosen by God to protect Kevin, she drives to Gates' recycling plant. Mulder, however, believes Gates will try to get out of town as quickly as possible, and heads for the airport. Scully's hunch proves correct; Gates throws himself into the blades of a gigantic recycling vat, taking Kevin with him. The boy, however, manages to cling to a safety platform and Scully pulls him to safety. The wounds on Kevin's hands miraculously heal.