“Paper Clip” is episode two of season three of The X-Files.
In the previous episode, “The Blessing Way”, Scully was told at William Mulder’s funeral by one of the Smoking Man’s group – called the Well-Manicured Man – that someone would be sent to kill her. Either someone she knew, or a team of two men. Scully was heading out to her sister’s place when Skinner stopped her, saying he needed to talk. Melissa, meanwhile, arrived at Scully’s and was shot by mistake by Krycek. Scully and Skinner had gone to Mulder’s; Skinner said he had the DAT. There was a noise outside and the two ended up pointing their guns at each other.
This episode opens with Albert Hosteen narrating, about how the FBI Man was cured by the Holy People, and the story of the Gila Monster, which is related to the healing powers of the medicine man. In the northern plains there is a story about White Buffalo Woman, and the northern people reported the birth of a white buffalo.
Skinner and Scully are both telling each other to put down their weapon; Scully thinks he is setting her up whilst he says he is trying to help. He didn’t come to kill her. Then Mulder comes into the room with his own gun pointed at Skinner. Skinner is convinced to put his gun down. Scully explains about how she was told someone would kill her, someone she trusted. Skinner says that the DAT is in his coat pocket. He also wants an explanation. Mulder states that the Smoking Man killed his father for the tape, then Mulder himself. He got better. The tape has DoD files that are not supposed to exist; evidence of a global conspiracy of silence regarding the existence of extra-terrestrials. It’s valuable enough to kill for, and the only leverage they have. Skinner convinces them to let him keep the tape, and Mulder and Scully leave.
Scully’s mother arrives at the hospital looking for Dana only to discover it’s Melissa there. She has a cranial gunshot wound and is in a medically induced coma. She wants to know if Melissa will be alright and the doctor tells her a lot of things that essentially boil down to ‘We don’t know.’
Mulder and Scully are with Byers and Langly looking at a photo containing Mulder’s father taken in 1973. Operation Paper Clip is mentioned, for one of the men in the picture is Victor Klemper; not one of the most famous criminals but perhaps the evillest war criminal to escape the trials for his experiments, which helped the U.S. win the Space Race. Even though Paper Clip was supposedly scrapped in the Fifties. Frohike arrives at this point; he had been at the hospital, having heard about Melissa’s shooting. Scully wants to head there but Mulder warns her that’s the first place they’d look.
The Smoking Man is in New York City meeting with the rest of the group. They are not impressed that Krycek shot Melissa. He promises to rectify it and insists that Mulder is dead. He also states he has the DAT, and is asked to show it. The Smoking Man acts annoyed that his honesty is being questioned. Even though he’s lying.
Mulder and Scully head to see Victor Klemper. He recognises Mulder’s name. He explains that he was a young man caught in a fervour, with others, but what he did advanced the world. Soon, he will die to. Mulder wants to know more about his father; Klemper tells him there are things he doesn’t need to know. On being pressed, Klemper asks if Scully is familiar with Napier’s constant and states the photo was taken at the Strughold Mining Facility in West Virginia. That’s all he will say. On them leaving, Klemper phones the Well-Manicured Man and tells him about the visit. The latter announces to the rest of the group – the Smoking Man is not there – that Mulder is still alive. They need to handle the matter.
The Strughold Mining Facility has been long abandoned and Mulder and Scully find a tunnel with a door that has a keypad whose code is Napier’s constant. Inside it are many filing cabinets. Many, many filing cabinets; both Mulder and Scully look stunned at the number when Mulder turns on the lights. The cabinets contain medical files, organised by year. Scully is there, and so is Samantha Mulder. Only her file originally read Fox.
Melissa’s hospital bed is being watched by someone and Albert Hosteen arrives to speak to Mrs Scully, telling her that her daughter can’t come. Skinner arranges a meeting with the Smoking Man; he may have located the digital tape. But there is a great chance it could fall into the hands of people whose purposes do not match the Smoking Man’s own. The Smoking Man is getting rather annoyed with Skinner, telling him he does not make deals. Does Skinner understand?
So, there is a choice. Use the DAT to get Mulder and Scully their lives back. Or try to find out what’s in the files.