In a bit of back story, it is shown that one of the cult members (who have now completely uncovered the spacecraft in Canada) formerly served in the Persian Gulf War; he observed four super-soldiers take out an enemy position and considered them angels. In present day, Doggett is in a coma, Comer is in critical condition, William has been kidnapped, and Scully is angry at Skinner and thinks Kersh and Follmer are complicit in all of it. To that end, The Lone Gunmen agree not to identify the kidnapper to the FBI and instead help Scully to find William's location based on a cell phone Byers was able to tuck into his car seat. Scully and Reyes find the cult woman's car and the car seat in Pennsylvania, but she and William are both gone.
In Canada, parts of the spacecraft start moving and it ends up sealing two men inside of it. Follmer shows Reyes how Comer has written "jacket" on a piece of paper, and Scully recognizes that it's a reference to the alien artifact. Bringing the artifact to the hospital, Scully and Reyes revive Comer and he tells them that the cult believes that the spacecraft is a temple for the physical manifestation of God, and also that William is a miracle child who will fight the aliens' return unless his father is killed; Comer says the cult killed Mulder to fulfill the prophecy, and that the death of William will save mankind (apparently because he'll be in league with the aliens otherwise). The spacecraft reopens when William is brought to it, revealing that the two cult members have been burned to death.
Comer also dies, and the artifact goes missing. Doggett awakens and immediately tells Scully that "they're going to come for you, but you can't trust them" as a result of a dream or vision. Soon after, Scully is contacted by the cult leader. In meeting him, he says he thinks William is destined to lead the alien race and Mulder is the only thing preventing that; it seems Mulder is still alive, as he wants Scully to bring him confirmation of his death. The agents track the leader to the excavation site, where William has managed to activate the spacecraft. The cult members are killed as it blasts off, but William is left unscathed. Follmer is a little uncertain about the circumstances of Comer's death, while Kersh apparently helps the "Toothpick Man," who was seen just before Comer died, to cover up the matter. We also see that the Toothpick Man is a super-soldier.
Episode Body Count
At least seven soldiers: killed in a mortar blast during the Persian Gulf War. I've counted wartime deaths unless they're mass casualty counts, so I'll allow this.
Two cult members: found dead inside the spacecraft some time after they are sealed inside.
Agent Robert Comer: dies in a hospital, by murder according to Reyes.
At least 15 cult members: burnt to death when the spacecraft in Canada blasts off.
Cumulative Body Count (192/202 episodes, 1/2 movies)
Humans: 2,176Creatures: 130
Grand Total: 2,370