Retired Lieutenant Colonel Zeke Josepho recounts a strange experience during the Persian Gulf War and how he claims it brought him to God: as his squad was ambushed during the Battle of Al Busayyah and on the verge of defeat, four mysterious men showed up and defeated the enemy with astonishing ease. While Josepho thinks of them as guardian angels, they are revealed to be the almost-indestructible Super Soldiers. In the present, Josepho stands above the wreckage of a spacecraft in Canada.[2]
At the FBI, Brad Follmer (Cary Elwes) discloses to a room of agents that Dana Scully’s (Gillian Anderson) son William has been abducted. Follmer notes that The Lone Gunmen are identifying the woman who took the child and ran over John Doggett (Robert Patrick). However, Follmer leaves out any potential motive for these crimes, which causes a frustrated Scully to leave the room. Byers (Bruce Harwood) reveals that he put a cell phone in the baby’s belongings so they can track the Overcoat Woman; Monica Reyes (Annabeth Gish) and Scully head out to find William. The two eventually find William's car seat along with the cell phone in an abandoned SUV. Meanwhile, the Overcoat Woman reports to Josepho that she has William.
Scully goes to Agent Robert Comer, whom she was forced to shoot after his attempt on William's life, and uses the alien artifact to heal him. Comer explains that Josepho believes a physical manifestation of God exists inside the spacecraft. According to an ancient prophecy, William is destined to become the savior of humanity, but only if Fox Mulder (David Duchovny) is still alive. If he dies, William will instead lead the Colonists. Comer claims that Mulder was supposedly killed by the cult in order for the aliens to successfully invade; he tried to kill William to prevent him from causing humanity's destruction. Suddenly, a nurse and the Toothpick Man (Alan Dale) arrive and ask Reyes and Scully to leave. Comer ends up alone with the Toothpick Man.
Walter Skinner (Mitch Pileggi) later reports to Reyes and Scully that Comer has died. Reyes accuses Toothpick Man and others in the room of killing Comer. Meanwhile, Scully visits Doggett, who warns her not to trust the cultists. However, Scully goes to meet Josepho near Calgary. Josepho claims to be protecting William, but demands Mulder's head as collateral in exchange for the baby's release. When Josepho returns to the wreck site, the Overcoat Woman relates that the aperture of the craft began to glow when William started crying. The craft soon rises up out of the ground. Looking on the site from a distance, Scully and Reyes see the craft burst out of an enclosure and into space, lighting the ground beneath it on fire as it goes. The two find an unharmed William among the charred bodies of the cultists.
At FBI headquarters, Follmer asks Kersh to remove his name from the final report. Instead, Kersh rebukes him and goes in to see the Toothpick Man, who is revealed to be a Super Soldier
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