S3E2 · Paper Clip

Continuing from the previous episode, Dana Scully (Gillian Anderson) and Walter Skinner (Mitch Pileggi) hold each other at gunpoint. Fox Mulder (David Duchovny), the person lingering outside his apartment, bursts in and forces Skinner to put his gun down. He also demands that Skinner surrender the digital tape. Skinner insists on keeping the tape, saying it is their only leverage in exposing the conspiracy.

The agents visit The Lone Gunmen, showing them an old photo featuring Bill Mulder, The Smoking Man, Deep Throat and other members of the Syndicate. The Lone Gunmen also recognize Victor Klemper, a notorious Nazi scientist who was brought to the United States under Operation Paperclip. Melvin Frohike informs Scully of her sister Melissa 's condition. Mulder persuades Scully not to visit Melissa at the hospital, since she could be targeted there.

Furious that the wrong person was murdered, the Syndicate demands that the Smoking Man produce the tape. The Smoking Man promises to do so the following day. Meanwhile, Mulder and Scully visit Klemper, who says that the photo was taken at Strughold Mining Facility, a former mine in West Virginia. After the agents leave, Klemper calls the Well-Manicured Man and informs him that Mulder is alive. The news causes the Syndicate to further mistrust the Smoking Man. Meanwhile, at the hospital, Albert Hosteen visits Melissa while a suited man loiters nearby.

Mulder and Scully arrive at the mining facility and, using the code for Napier's constant given to them by Klemper, unlock one of the reinforced doors inside. They discover a large complex of filing cabinets containing smallpox vaccination records and tissue samples. Mulder finds his sister Samantha 's file and finds that it was originally meant for him. Meanwhile, Skinner tells the Smoking Man that he may have found the digital tape. The Smoking Man is agitated at this, insisting that he will not make a deal with Skinner and tacitly threatening his life.

Hearing a noise, Mulder heads outside and witnesses a UFO flying overhead; inside, small beings run past Scully. Cars full of armed soldiers arrive, forcing the agents to flee. They meet with Skinner at a diner in rural Maryland. Skinner wants to turn over the tape in exchange for their reinstatement and safety. After initially objecting, Mulder agrees. Skinner heads to see Melissa in the hospital and is told by Hosteen of the suited man outside. Skinner chases the man into a stairwell, where he is attacked by Alex Krycek and Luis Cardinal, who beat him unconscious and steal the tape.

Krycek narrowly escapes an attempt on his life when his car explodes. He subsequently phones the Smoking Man, telling him that he has the tape and will make its contents public should anyone come after him. The Smoking Man lies to the rest of the Syndicate, telling them that Scully's would-be assassin was killed in the car bombing and that the tape has been destroyed with him. Mulder and Scully return to Klemper's greenhouse, finding the Well-Manicured Man there. He admits to knowing Mulder's father and states that he helped gather genetic data for post-apocalyptic identification, data Klemper used to work on alien-human hybrids. Samantha was taken to ensure Bill Mulder's silence after he learned of the experiments.

Mulder confronts his mother, who tells him that his father chose that Samantha be taken. At FBI headquarters, Skinner once again meets with the Smoking Man about the tape. The Smoking Man calls Skinner's bluff, knowing he no longer has the tape, but Skinner reveals that Hosteen and twenty other Navajo have memorized its contents and are ready to reveal it if either Mulder or Scully are harmed. Mulder meets with Scully at the hospital, who reveals that her sister died a few hours before. Mulder tells Scully that he believes that the truth is still in the X-Files. Scully tells him that she's heard the truth, and now what she wants are the answers.