Kevin travels with his mother in a car that breaks down. Scully finds that handprints on Owen's neck belong to Simon Gates, a rich and powerful executive. Mulder tells Scully to not let her faith cloud her judgement. Scully performs an autopsy and finds that Owen's corpse is not decaying, reminding her of "incorruptibles" that she learned about in Catechism. Kevin arrives at his home and is pursued by the man who killed the priest, who kills Owen when he arrives to protect him. Owen claims he was asked by God to protect Kevin and criticizes Scully for her faith not being as strong as his. By the time the agents arrive Kevin is gone. Owen claims to be Kevin's guardian angel.
Kevin's mother recognizes the man's description as Owen Jarvis, who had done yard work for the family in the past. Kevin is abducted by a strange-looking bald man. The agents visit Kevin's father, who claims that his son is the chosen one and that evil forces will come to kill him as part of a great war between good and evil. The agents arrive and meet with a social worker, who claims that Kevin has suffered injuries before and that his father was institutionalized, claiming that Kevin was in danger from evil forces. Meanwhile at an elementary school in Ohio a boy, Kevin Kryder starts bleeding from the palms of his hands.
Mulder says that the reverend was the eleventh fake stigmatic who has been killed over the past 3 years in a series of international murders. He says that the sermon really touched him, and praises the reverend. After service, a parishioner comes in to see the reverend in his dressing room. As his sermon nears its end, he begins bleeding from his hands. In Waynesburg, Pennsylvania, a reverend is giving a sermon about the importance of faith in an increasingly cynical world. Mulder and Scully investigate a series of murders that may be related to stigmata and Scully questions her faith.