Post mortems conducted on the previous victims proved inconclusive, the post mortem performed on Karens body, found that the two mysterious marks on her back had an unidentifiable protein residue surrounding it, similar to at least two other recorded cases of alien abduction elsewhere in the USA.
The body of the 3rd victim, Ray Soames is exhumed for further investigation, it is shrunken and mutated. Scully autopsys it and concludes that it is not of human origin but of mammalian physiology. Also, she finds a strange metallic object hidden in the nasal cavity. The agents investigation is met with resistance from the locals, especially Dr Jay Nemman, who performed the autopsys on the previous victims and Detective Miles... who know more than what they're letting on!!!
The agents visit the local psychoratic hospital to get more information on Ray Soames, they discover that another two former classmates: Billy Miles and Peggy O'Dell are residents there following a car crash, leaving Billy in a waking coma and Peggy in a wheelchair. Mulder discovers that Peggy also has the same two marks on her back, as the ones discovered on the body of Karen Swinson. Mulder believes they're victims of alien abduction, which Scully rejects.
Back at the hotel, there's a power cut. Unable to do any work, Scully runs a bath. Whilst undressing, she discovers bumps on her back. Worried, she rushes to Mulders room and gets him to examine her back... she's told they're only mosquito bites. Relieved, she hugs him. Later on, Mulder opens up to Scully about his sister Samanthas mysterious disappearance when he was 12 and why he got interested in The X-Files. Whilst they're chatting, the phone rings... Peggy O'Dell has died!!!
At the scene of the accident, they discover she'd been run over, not unusual but for the fact that Peggy was in a wheelchair. Scully looks over the body and notes that Peggys watch stopped at 9:03, the same time that she and Mulder had the unexplained 9 minutes of time loss. With the death of Peggy; the destruction of all there evidence, and Theresa Nemmans plea for help. Makes the agents more determined to find out the truth. Mulder believes that Billy is responsible for the murders, Scully concludes that it's impossible because he's been in a coma for the past 4 years. Undeterred, they return to the hospital, Scully discovers that Billys feet are covered in dirt from the forest. After a night-time chase through the forest, an armed confrontation reveals all.
Under questioning, Billy explains what happened. He tells them about the graduation party in the forest and how there was a light, and it took him away, to a testing place. They put something inside his head and he had to await his orders, orders from the light. The light told him to gather the others for testing but the tests didn't work and the evidence was destroyed. Scully reports back to Section Chief Blevins with her findings, her report is dismissed due to lack of evidence and inconsistencies. Scully produces the metallic object she extracted from the nasal cavity of Ray Soames, and the only piece of evidence to survive the hotel fire, from her pocket "This is the object described by Billy Miles as a communication device. I ran a lab test on it. The material could not be identified". Section Chief Blevins looks at the object and Scully is dismissed from his office, passing the smoking man in the corridor.
The smoking man is seen walking down a long corridor of shelves with boxes on them, he stops and places the metallic object in Box No. 100041, which is full of similar material. He continues and locks the door, it turns out to be a basement in the Pentagon.
