As Doggett recovers from injuries in hospital, Reyes and the Lone Gunmen help Scully in an effort to recover her baby.
Retired U.S. Army Lieutenant Colonel Zeke Josepho recounts his strange encounter during the Persian Gulf War in February 1991 and how it brought him to God. He and his soldiers were ambushed and all of his men, but him, were killed. He remembers seeing four men who were not men showing up and defeating the enemy with complete ease. While Josepho thinks of them as guardian angels, they were "super soldiers" who were nearly indestructible.
Josepho stands above the strange aperture at the top of the spacecraft newly uncovered by the excavation of the cult members.
A.D. Follmer discloses to a room of FBI special agents the current situation: Agent Dana Scully’s son William has been abducted. The Lone Gunmen are identifying the woman who took the child and also ran over Agent John Doggett, who is now in a coma. He mentions Agent Comer’s attack on the child as well but Follmer excludes any motive for these crimes. A frustrated Scully leaves the room.
A.D. Skinner follows her and they have an argument. Scully accuses Skinner of holding out on her with reports of Fox Mulder’s potential demise. She believes that D.D. Kersh, Follmer, and Skinner are part of a conspiracy to obscure the truth. Skinner denies this and goes to check on Agent Doggett. Agent Monica Reyes is watching over him and Skinner tells her he probably can feel her holding his hand and hear her talking to him in the coma.
Scully asks Reyes to see her alone. Reyes arrives and learns the Lone Gunmen refused to identify the woman who took William. Scully asked them to do this and is now asking Reyes to quietly look into the woman’s background. However, John Byers of the LG put a cell phone in with the baby’s things so they can track the woman. They track the signal’s source and Reyes and Scully head out to find William.
Overcoat Woman reports that she has William to Josepho. The aperture of the ship seals two men inside and Josepho and his cultists scramble to get them out of there.
Scully and Reyes find the car seat( with the cell phone Byers planted) in the deserted van but no sign of the woman or William.
Follmer finds Reyes praying and shows her that Comer had the word “Jacket” written down. When Reyes tells Scully about this she realizes that he wants the alien artifact to be used to heal him. Comer is revived and reveals his secrets.
He was sent undercover within the cult of Josepho. This cult believes that aliens will soon rule the world and Josepho led them all to the site of an alien craft far to the north. Josepho claims to speak to God and that the craft they are now excavating (the artifact is from this specific craft) is a temple that holds the physical manifestation of God. Josepho ordered Comer to seek out William but to protect him, at least until it was learned Mulder was dead. Apparently a prophecy says William is some savior of mankind but only if Mulder is still alive, otherwise he is not and he will lead the forces of evil.
A nurse and some FBI agents come in and ask Reyes and Scully what they are doing there. Scully says Comer no longer needed the life support machines. The lead agent demands that Skinner and Follmer come down immediately. The lead agent (Toothpick Man) is alone with Comer and the sick man seems terrified about that.
Overcoat Woman arrives with William and then the aperture opens revealing the two men burned to death.
An angry Follmer and Skinner arrive downstairs but Reyes and Scully ignored orders and left. Follmer tells Skinner they need them now. Reyes and Scully have a discussion about the things that Comer said and while Scully believed it, Reyes dissuades Scully from believing it, suggesting that everything the cult (and Comer) believes is wrong and Scully shouldn’t buy into it.. Skinner shows up and calls them back to Comer’s room saying that Comer has died. Reyes returns and accuses Toothpick Man and the others in the room of doing something to Comer but she comes off badly to the agents there. Meanwhile Scully is with Doggett who wakes up and tells her: “They’re going to come to you, but you can’t trust them.” Right after he says that, Josepho contacts her and wants to meet with her.
Scully goes to meet with them near Calgary, Canada. Josepho claims to be protecting the infant and says the super soldiers are the true sons of God. He says William will lead the alien race that is coming. He demands confirmation that Mulder is dead since he now doubts Mulder’s demise and only the head of Mulder will free William.
The Lone Gunmen place a tracking device on Josepho’s truck and Reyes and Scully pursue the man when he leaves.
As Josepho returns, Overcoat Woman relates that the aperture started glowing after the baby started crying. It becomes a pillar of light as the cultists are gathered around. The craft begins to rise up out of the ground.
Scully and Reyes see a craft burst out of the enclosure, lighting it on fire as it goes; it flies out into space. A desperate Scully runs through the fiery wreckage finding the burned bodies of cult members everywhere. Reyes signals Scully to be quiet for a moment and they hear a baby crying. They find a miraculously unharmed William among the debris.
Doggett talks with Reyes in the hospital church about how a voice in his head kept telling him to wake up and warn Scully. He asks if Reyes told him that but she says she only prayed for his life.
Follmer comes to Kersh about how Comer’s vital signs improved just before his monitors were turned off. Kersh asks what Follmer wants then and Follmer says he wants his name taken off the report. Kersh rebukes him and goes in to see the Toothpick Man. We see that he has the vertebrae marks on his neck, like any super soldier.
- When Lieutenant Colonel Zeke Josepho is calling in his contact report he makes the same old Hollywood error of using the word 'REPEAT' over the radio. The correct terminology to use is, "I SAY AGAIN' and you only do so if the person you're talking to asks for a confirmation of your message. It is an age old Hollywood cliché that a whenever a character speaks on a radio they have to relay the message twice to accentuate the drama.
- In the diner, when Lieutenant Colonel Zeke Josepho quotes a passage from the Bible, he is partially quoting, from the prophetic book of Ezekiel chapter 1, verses 4-8------
- (4) And I looked, and, behold, a whirlwind came out of the north, a great cloud, and a fire infolding itself, and a brightness was about it, and out of the midst thereof as the color of amber, out of the midst of the fire.(5) Also out of the midst thereof came the likeness of four living creatures. And this was their appearance; they had the likeness of a man.(6) And every one had four faces, and every one had four wings.(7) And their feet were straight feet; and the sole of their feet was like the sole of a calf's foot: and they sparkled like the color of burnished brass.(8) And they had the hands of a man under their wings on their four sides; and they four had their faces and their wings.
- They are also referenced in another prophetic Biblical book, the book of The Revelation of Jesus Christ: Revelation 4:5-8-----
- (5) And out of the throne proceeded lightnings and thunderings and voices: and there were seven lamps of fire burning before the throne, which are the seven Spirits of God.(6) And before the throne there was a sea of glass like unto crystal: and in the midst of the throne, and round about the throne, were four beasts full of eyes before and behind.(7) And the first beast was like a lion, and the second beast like a calf, and the third beast had a face as a man, and the fourth beast was like a flying eagle.(8) And the four beasts had each of them six wings about him; and they were full of eyes within: and they rest not day and night, saying, Holy, holy, holy, Lord God Almighty, which was, and is, and is to come.
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- Annabeth Gish as Special Agent Monica Reyes
- Mitch Pileggi as Assistant Director Walter Skinner
- Cary Elwes as Assistant Director Brad Follmer
- Bruce Harwood as John Fitzgerald Byers
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Neal McDonough as Agent Robert Comer
- McNally Sagal as Overcoat Woman
- Denis Forest as Lt. Colonel Zeke Josepho
- Alan Dale as Toothpick Man
- Kerrie Keane as Nurse
- Jamie McShane as Injured Soldier
- Brian Morri as First Soldier
- Christian Hastings as Second Soldier
- Brad Kalas as First Cult Man
- Kevin McCorkle as Second Cult Man
- James Riker and Travis Riker as William Scully III