Things are starting to heat up now and anything can happen. We start with someone making a break for the American border from Canada, only to die in the process, but as the body lays burnt on the floor, we see a stone of some sort, with the alien writing engraved on it that Scully found on a space craft in Africa. Scully is called into Kersh’s office where Skinner, Kersh, Agent Follmer and a few other old hacks integrate her about the rubbing’s she found two years ago, she doesn’t give them much information, and they reveal nothing in return. So naturally Doggett and Monica start their own investigation.
Monica works through the rubbing’s that Scully took from Africa, and Doggett heads out to the site where the new ones were discovered. Follmer happens to already be at the scene, and warns Doggett about perusing an investigation, while Monica compares notes with Scully. She explains that the words written are basically the words of god - written many years ago and appeared on a space craft - the Bible and the Koran may indeed all just come from space!
Meanwhile, we see the guy riding the motorbike at the beginning, recover from his wounds by clutching a small metal object with the alien symbols on it. Doggett finds out (by breaking into Skinners office) that the man riding the bike and carrying the symbols was an FBI agent called Robert Comer, he was sent deep undercover to investigate a religious group working in North Dakota and then moved up to Canada. The FBI can’t find him and have been keeping everything rather hush.
Scully heads home to find Mummy Scully being kicked around by the FBI Agent known as Robert Comer (after just meeting with Doggett and Monica to get this information.) Comer wants to kill William! He locks Scully out and attempts to smother William with a pillow until Scully shoots him a few times. Slightly upset, she calls Doggett and Monica who turn up to find everyone bleeding, but no ambulance. She attempts to interrogate him but all he knows is that William must die. Scully looks through his jacket after he’s gone to hospital and finds the metal he had with symbols on it.
Anyway, word gets around that Robert Comer was shot and we see a mysterious woman talking to a mysterious man who’s been digging at some site in Canada - digging up another UFO space ship!
Scully and Doggett get called into Kersh’s office once again, only this time, information flows a little more freely. Kersh explains that Comer was sent undercover etc etc, stuff Doggett already found out by snooping through Skinners office, but he goes on to explain that the religious cult is ran by a former military officer who had rather dangerous ideas about aliens.
Skinner didn’t want Scully to investigate it because he was afraid it might break her, when questioned what that means, Kersh states they were investigating the cult based on death threats made to… Mulder! It makes little sense to Scully, but Follmer states that the last communication from their undercover agent was that Mulder is already dead. Scully storms out the room nearly in tears.
Monica goes to see a rather upset Scully when they hear a rattling coming from the draw where she’s stored the metal object. On opening the draw, the metal object shoots out, breaks through William’s cot and circles above his head. Monica tries to explain to Doggett that there is a connection between William and what’s going on because of this, and that the metal object- most likely part of the space craft, is attracted to William.
With that, they need to get William to safety - So Scully and Monica head out to meet the Lone Gunmen! They give William to them who assure Scully they’ve taken all precautions, Doggett notices that the weird unknown woman was watching them leave Scully’s apartment and attempts to question her… only to get ran over.
Scully and Monica return to her apartment to find Doggett lying in the middle of the road, Scully realises that they must now know where William is and as the Lone Gunmen head away from their meeting point - they are cut off and shot at by the weird unknown woman - who opens the Volkswagen door and puts a gun to Byers’ head. End of part 1!