At the FBI, the Toothpick Man watches as the Lone Gunmen scan the mug shots of suspects who may have taken Scully’s baby. Meanwhile, A.D. Follmer briefs a task force about William’s kidnapping and Doggett’s near death in the ensuing attack. Scully is appalled at Follmer whitewashing the investigation, and she leaves in a huff. When Skinner stops her, she accuses the FBI of attempting to rid any element of the X-files – which includes not only Doggett and Mulder, but also her son. Skinner bristles at her allegations, but he is still concerned for Scully.
Reyes stands vigil as Doggett lays in a coma at St. Mary’s Hospital. When Skinner visits, Reyes gets a call from Scully. Scully asks to meet her, but not tell Skinner. Reyes arrives at Scully’s apartment, where the Gunmen are working at a laptop. They identified the overcoat woman kidnapper, but did not tell the FBI. Byers had been able to tuck a cell phone into William’s car seat, and they hope to track the phone’s signal and find the baby. The signal is coming from Warfordsburg, Pennsylvania, and Scully sets off with her gun in pursuit of William. Reyes follows.
In Pennsylvania, the overcoat woman leaves William in the car to make a call at a pay phone. She dials Josepho, who is watching a group of cult members try to pry open the spaceship’s hull from underneath its fins. When she informs Josepho that she has the child, the fins of the spaceship interlock, trapping the workers under a dome on the craft. Scully and Reyes finally arrive at the pay phone location, and while the car is still there, the overcoat woman and William have disappeared. The baby seat and cell phone remain in the back of the car.
Reyes returns to St. Mary’s, and prays in the hospital chapel for Doggett’s recovery. Follmer finds here there, and informs her that he knows that she went after the kidnapper. He is aware that there are forces within the FBI working against them, but Follmer swears that he is indeed on her side. Follmer now needs her help. Robert Comer, the FBI agent who Scully shot in 9X10, has woken up and has written the word “jacket” on a notepad. Follmer wants Reyes to find out from Scully what that word means. Reyes approaches Scully with the paper, but Scully refuses to tell the FBI what she knows. Comer had been carrying the artifact from the spaceship in his jacket. That artifact may have healed his wounds from the motorcycle accident at the Canada border. Reyes follows Scully back to the hospital, where they sneak into Comer’s room. Scully waves the artifact over Comer’s gunshot wounds, and his heartbeat spikes. He awakens, and grabs Scully’s arm. She threatens to kill him unless he explains why he wanted her baby. Comer explains that Josepho is the leader of a cult whose followers believe that an alien race will rule the world. The spaceship they found is a physical manifestation of God. God spoke to Josepho, and told him that William is a future savior who will try to prevent the aliens’ return — just like his father attempted. William will succeed at stopping this colonization unless his father, Mulder, is put to death. To fulfill the prophecy, Mulder was killed. Josepho now wants to protect William, but Comer has come to rid of William with his own plans to prevent the aliens from taking over the world. Comer reaches for the artifact to complete his healing when a nurse walks in with the Toothpick Man. Scully covers the bed sheet over the artifact. The Toothpick Man orders Scully and Reyes’ removal. As the others leave, he ominously remains in Comer’s room.
At the tent in Canada, Josepho’s men try to open the spaceship to save the cult members inside. When the overcoat woman enters the tent with William, the fins of the spaceship inexplicably open. The men who were trapped are revealed to be burned and smoking corpses.
Scully and Reyes hide out in the hospital’s chapel, and Scully admits her fears to Reyes that her son is an abomination meant to die. Reyes convinces Scully that this perception is only one man’s belief that may not even be true. Skinner comes in with news of Comer’s death. Because they are suspects, he advises them to leave immediately. Reyes rushes back to Comer’s room. Reyes pulls off Comer’s sheet, but the artifact is missing. Reyes wants the Toothpick Man searched for the artifact, and she looks to Scully to backup her account of the events. Scully, however, has gone to Doggett’s room. Doggett suddenly awakes from his coma, and tells Scully that he heard someone talking. Doggett warns Scully that someone is going to come to her, but that she shouldn’t trust him. Scully’s cell phone rings. It is Josepho, giving her strict instructions that she must obey in order to see her son.
Scully meets Josepho alone in a diner outside Calgary, Canada. He tells her that he has witnessed Super Soldiers, and that they are the true sons of God. Josepho believes that William will be the leader of the alien race that will rule the Earth. Although Josepho once believed that Mulder was dead, he now has doubts. He offers to give her William when she brings him confirmation of Mulder’s death. Mulder being alive is the one thing that will prevent William from leading the aliens. Scully accuses Josepho of lying, and he demands that she bring him the head of Mulder. Josepho walks out, and Scully quickly calls Reyes in a nearby van. She is with the Gunmen, who have wired Josepho’s car. As the Gunmen track Josepho, Reyes and Scully follow him. Yet the Gunmen lose the signal, and Scully is forced to blindly pull over. She sees a white tent in the distance and runs toward it. Meanwhile, inside the tent, William begins to cry. At the sound of his voice, the bezels on the spacecraft suddenly turn and drop into the ground. The ship then blasts a shaft of white light into the sky, and begins to vibrate and hum. The cult members watch as the spaceship starts to surface. Scully and Reyes see the ship take off into the night. The tent explodes into flames. They run to the tent’s remains, discovering charred bodies among the wreckage. They suddenly hear a baby’s cry. William is lying on the ground, unharmed.
Reyes finds Doggett in the chapel at St. Mary’s Hospital. He says that when he was in the coma, a voice told him to get up and warn Scully about this man. Doggett asks Reyes if it was she who was talking to him. She says no.
At the FBI, Follmer tells Kersh that he has recently learned that the monitors in Comer’s room show that the man’s vital signs returned back to normal right before his death. Follmer is befuddled, and has no explanation for this. The Toothpick Man is waiting in Kersh’s office, and Kersh hands him the case folder. Kersh then congratulates him because it now appears that everything from the case is dead. However, the case itself seems to still be active. “I’m sure I can take care of that,” the Toothpick Man replies. Unseen on the Toothpick Man’s neck is the familiar spiny ridges of an alien replacement.
Original Air Date: 03/10/02
Written by Chris Carter & Frank Spotnitz
Directed by Chris Carter
GILLIAN ANDERSON as Special Agent Dana Scully
ROBERT PATRICK as Special Agent John Doggett
ANNABETH GISH as Special Agent Monica Reyes
MITCH PILEGGI as A.D. Walter Skinner
James Pickens, Jr. as Deputy Director Kersh
Cary Elwes as A.D. Brad Follmer
Bruce Harwood as Byers
Tom Braidwood as Frohike
Dean Haglund as Langly
Neal McDonough as Agent Robert Comer
McNally Sagal as Overcoat Woman
Denis Forest as Josepho
Alan Dale as Toothpick Man
Kerrie Keane as Nurse
Jamie McShane as Injured Soldier
Brian Morri as Soldier #1
Christian Hastings as Soldier #2
Brad Kalas as Cult Man
Kevin McCorkle as Cult Man #2
James Riker as Baby William
Travis Riker as Baby William