There used to be a time when religion had no place in the X-Files, however with this episode, I don’t even know where to start. Part 2 basically covers super soldiers, god, and aliens when we start with a nice little summary of events.
Scully’s baby has been taken by an unknown woman, Doggett is in a coma after being hit by a car, and Follmer is leading the investigation into it. The actual episode starts with a voice over from the man who leads the crazy UFO cult, telling us about when he first came to believe in more then what the eye sees. He was at war and despite everything looking rather bleak - four guys came out of nowhere, withstood bullets and an explosion, to save him.
Scully asks the Lone Gunmen to identify the woman who took William, she’s part of the UFO cult Comer was investigating. Scully tells Monica to get any information on the woman quietly, and that they’ve got a location for her since Byers hid a phone in Williams baby seat before being taken. We then see the UFO cult leader talking to the woman, stating that they have the baby alive and well, and that now they can finally protect William.
Monica goes to see a rather comatose Doggett, who then prays for his life - she’s interrupted by Agent Follmer who states that Comer wrote the words ‘Jacket’ on a bit of paper, she shares this information with Brad who doesn’t make Scully too happy and states that Monica has ‘learned absolute nothing from her’. They take the object to Comer who comes back to full good health - and here’s where the complicated bit comes in.
Comer states that he was investigating the UFO cult who believe that aliens will one day rule the world, and that god told the leader to head to Canada and dig up the space ship - which contains the physical form of god. He also said that god told the leader that there will be a miracle child, coveted by good and evil forces, and that the cult wants to protect him. You see, they believe that the child will follow in it’s fathers footsteps (Mulder!) and try to stop the aliens from taking over, unless his father was to be killed.
Scully thinks now that Mulder is actually dead and that they killed him to fulfil the prophecy, and that William must die or everyone on earth will. Make much sense? It took me a while but if you think about it, the child can be used by good and evil - it hasn’t been decided yet. William can either lead the aliens - or stop them. Since Mulder was intent on stopping them (mostly unintentionally, he just didn’t have a clue what was going on most of the time!), they can raise William to lead instead of revolt.
At this point Monica and Scully are interrupted by an unknown man who seems to pull rank on both Skinner and Follmer. Monica tries to talk Scully out of believing the nonsense but Scully can’t deny what she has seen to support its claim. Then they get news that Comer has died shortly after speaking to him. Monica gets her first glimpse of cover up when the object that Comer had to heal himself mysteriously disappears and that everyone in the room is accusing her.
Scully prays beside Doggett who happens to wake up and say that the voices in his head were guiding him, and that Scully is about to be contacted - but she must not believe them. What do you know?! Scully is contacted by phone and asked to follow instructions if she wants to see William again.
She heads to a bar in Canada and meets with the UFO cult leader. He assures Scully that William is safe and being protected. After quoting the bible he states that William will lead the alien race (guess that makes the UFO cults’ intentions clear). He’ll take Scully to William only if she brings him something. Conformation that Mulder is dead.
Scully was pretty sure they killed Mulder, but the leader corrects her. He says that if Mulder is alive, he’s the one thing preventing her sons true destiny. Summed up, if she wants to see William - Scully must bring the head of Fox Mulder!
Time for the Lone Gunmen to kick ass! They bug the leaders car while in the bar and they follow him out to the woods. After loosing the signal, they find the small white tent which has been hiding the site where the UFO cult were digging out the space craft. As they approach, we see the thing light up, and rise, flying off into the night, leaving a fire and charred bodies behind. Scully fears the worst and runs in, to find William crying on the floor.
We end the episode with a twist in Follmer’s character. He confronts Kersh who is holding the investigation into Comers death, and states that Skinner didn’t sign it because he believes someone murdered him. Follmer signed the report stating it was natural however he did notice something strange. Before the monitors went off, Comer’s condition improved back to normal health. Because of this he can only conclude murder, but can’t explain it, and requests his name be taken off the report.
Kersh heads back into the office looking disappointed and speaks to an unknown man, congratulating him on making everything disappear regarding the case. It’s the same man that ordered Scully and Monica out of Comers room, and that Monica accused of murdering him. The last scene is of the back of his neck….. he’s a hybrid!