As Scully desperately searches for her son, religious cult members prepare to enter a spaceship which they believe houses God.
As Operation Desert Storm unfolds, Captain Zeke Josepho is thrown to the ground by an explosion. Several of his men are killed. Josepho sees four soldiers rush through the building, unaffected by enemy fire and explosions. We see an older Josepho working at the Canadian dig introduced in the previous episode as he helps unearth the buried spaceship.
At FBI headquarters, Brad Follmer briefs a team of agents on the abduction of Scully�s baby, telling them that Doggett is in a coma after being run over, while FBI Agent Robert Comer is also in critical condition after being shot by Scully. Scully identifies the Overcoat Woman with the Lone Gunmen's help.
It�s revealed that Byers managed to slip a cell phone under baby William�s car seat duringhis abduction. The Gunmen pinpoint the car through the phone system, finding it in Warfordsburg, Pennsylvania. By the time Scully and Reyes arrive, though, the baby and the abductor have vanished.
Back at the Canadian dig, a cylindrical bezel rotates around two cult members and then lowers them into the ship. At the hospital, Comer writes the word, "jacket." When Reyes relays this to Scully, she deduces that Comer means the jacket he was wearing when she shot him.
Scully brings the alien artefact in Comer�s jacket to his hospital room. Comer suddenly grabs Scully�s wrist and lowers the artefact to his chest. Scully instructs Reyes to unplug the life support monitors so the hospital staff aren�t alerted to the situation.
When Comer revives, he tells Scully that her son must die and describes Josepho�s belief that the alien ship houses a physical manifestation of God. Josepho also believes baby William will follow in Mulder�s footsteps and try to stop the aliens� return. According to Comer, Mulder was killed to fulfill the prophesy, and unless baby William is killed, all mankind will perish. Suddenly, a nurse and the Toothpick Man enter the hospital room and demand to know what�s going on.
At the alien dig, the bezel rotates once more, and emerges from the ship with two charred corpses on it - the men seen before. Follmer informs Scully and Reyes that the nurse is claiming they killed Comer by pulling him off life support. Outraged, Reyes bursts into Comer�s room and demands to know the location of the alien artefact, but the nurse and the Toothpick Man claim to have no knowledge of its existence.
Josepho arranges a meeting with Scully outside Calgary, Canada. He tells Scully she can have baby William if she brings him the head of Fox Mulder. The Lone Gunmen attach a magnetic transponder to his car to track his whereabouts, but the device goes dead � perhaps because of interference from the ship.
Back at the dig, an opening appears in the ship, giving Josepho hope that he can view the face of God. A blast of light shoots out of the hole, illuminating the night sky and clueing Scully to the dig�s location. The ship then rises into the air, incinerating the cult members. Scully arrives at the scene and finds William, the sole survivor.
At FBI headquarters, Skinner tells Kersh that Comer�s vital signs improved dramatically before he died, confirming Reyes� and Scully�s story. Leaving the meeting, Skinner makes eye contact with the Toothpick Man... and we see spiny ridges on the back of his neck.
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