S3E11 · Revelations

A minister named Reverend Patrick Findley (R. Lee Ermey) in Waynesburg, Pennsylvania fakes stigmatic injuries to his hands during a sermon. Afterwards, Reverend Findley is visited by a white-haired man named Simon Gates, who strangles him—his hands smoking while he does so. Agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) investigate the case. Mulder says that the minister was the eleventh fake stigmatic who has been killed over the past three years in a series of international murders. Meanwhile, at an elementary school in Loveland, Ohio, a boy, Kevin Kryder starts bleeding from the palms of his hands.

The agents arrive and meet with a social worker, who claims that Kevin has suffered injuries before and that his father was institutionalized, adding that Kevin was in danger from evil forces. 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".

Kevin is abducted by a strange-looking bald man. Kevin's mother recognizes the man's description as that of Owen Jarvis (Michael Berryman), who had done yard work for the family in the past. Owen claims to be Kevin's guardian angel. As the agents arrive, Kevin mysteriously disappears. Owen claims he was asked by God to protect Kevin and criticizes Scully for her faith not being as strong as his. Owen jumps out the window and escapes. Kevin arrives at his home and is pursued by Gates, who kills Owen when he arrives to protect Kevin. Scully performs an autopsy and finds that Owen's corpse is not decaying, reminding her of "incorruptibles" that she learned about in Catechism. Mulder tells Scully to not let her faith cloud her judgment. Scully finds that handprints on Owen's neck belong to Simon Gates, a rich and powerful executive.

Kevin travels with his mother in a car which breaks down. Gates arrives offering to help fix the car, and Kevin, who appears in two places at once, is able to distract him and help them escape. However, Kevin's mother - becoming faint after being hurt by Gates - runs the car into a ditch and dies as a result. Scully tells Kevin she'll protect him. They bring him to a hotel where Scully notices an additional wound on Kevin's side. Scully becomes upset that Mulder will not even consider that a miracle is possible. As they talk, Gates breaks into the bathroom, kidnapping Kevin by prying an opening in the barred window. Scully returns to see Kevin's father but finds him heavily drugged.

Scully theorizes that Gates has brought Kevin to a recycling plant he owns in Jerusalem, Ohio. Mulder thinks that he has headed to the airport, as a man matching Gates' description was reported headed there. Mulder thinks Scully believes that she's been chosen to protect Kevin. Scully arrives at the recycling plant where Gates tells Kevin that he must die for the 'New Age' to come. Gates attempts to jump into a paper shredding machine with Kevin, but Kevin grabs on to the side as Gates falls into the shredder and is killed. Scully is able to pull Kevin to safety. Two days later, Scully and Kevin say goodbye; Kevin tells Scully he'll see her again.

Scully goes to confession for the first time in six years, admitting that she was raised a Catholic but has drifted away from the Church since then. She admits to being unsettled by the things she has witnessed, and even more unsettled by the fact that Mulder, usually the more credulous of the two of them, has not seen them. The priest advises her "Sometimes we must come full circle to find the truth" (unconsciously echoing the recycling symbol Scully has seen several times earlier in the episode) and asks her if she is starting to doubt her own judgment. Scully says that mostly it makes her afraid: that if miracles really do occur, then that means "God is speaking... but that no one's listening."