PAPER CLIP

                                         Mulder is dead....I took care of it myself

Continuing from the previous episode, Dana Scully and Assistant Director Walter Skinner hold each other at gunpoint. Fox Mulder is revealed to be the person outside his apartment and bursts in, convincing Skinner to put his gun down. Skinner tells them the digital tape is their only form of leverage and they decide to let him hold onto it for the time being.

Scully's mother arrives at the hospital and is surprised to find that Melissa is the one there instead of Dana, suffering from a gunshot wound to the head. Mulder brings a photo from the 1970s to the Lone Gunmen, showing Mulder's father, the Cigarette Smoking Man, Deep Throat and others. The Lone Gunmen recognize one of the men as Victor Klemper, a Nazi scientist who came to the U.S. after World War II and was given immunity from prosecution under operation Paper Clip. Frohike arrives and tells Scully that her sister is in the hospital, but Mulder convinces her not to go, since her life would be in danger there. Meanwhile the Syndicate meets, upset over the fact that an innocent woman has been shot by mistake. The Well Manicured Man demands that the Cigarette Smoking Man provide them with the digital tape, to which he replies he will bring it tomorrow.

Mulder and Scully visit Klemper in his greenhouse, who admits that the photo was taken at the Strughold Mining Company in West Virginia. After they leave he calls the Well Manicured Man, who learns that Mulder is alive. Albert comes to see Melissa in the hospital while a mysterious man in a blue suit waits outside. Mulder and Scully arrive at the mining site and using the code for Napier's constant, told to them by Klemper, are able to head inside. Skinner tells the Cigarette Smoking Man that he may have the tape, a fact that makes the Cigarette Smoking Man very upset, threatening Skinner's life. Mulder and Scully find a large complex of filing cabinets containing smallpox vaccination records and tissue samples. Mulder finds his sister's file and finds that it was originally meant for him. Hearing noise, Mulder heads outside where he witnesses a U.F.O. flying overhead. Small beings run past Scully. Cars full of armed soldiers arrive, and the agents flee.

Mulder and Scully meet with Skinner at a diner in Maryland. Skinner wants to turn over the digital tape in exchange for their reinstatement and safety. After initially objecting, Mulder agrees to let Skinner turn the digital tape over. Skinner heads to see Melissa in the hospital and is told by Albert of the mysterious blue-suited man who has been waiting outside. Skinner chases the man to a stairwell where he is beaten up by Alex Krycek and Luis Cardinal, who steal the digital tape. Krycek and the others flee, and Krycek narrowly escapes an attempt at his life when the car he is in blows up after the other two leave the car at a gas station. Mulder and Scully return to Klemper's greenhouse, finding the Well Manicured Man there. He admits to knowing Mulder's father and states that during the cold war Mulder's father helped gather genetic data for post-apocalyptic identification – data which was used by Klemper to work on alien-human hybrids. When Mulder's father learned of this, he threatened to expose them, so Samantha was taken to ensure his silence.

Krycek phones the Cigarette Smoking Man, telling him that he has the tape. The Cigarette Smoking Man lies to the rest of the Syndicate, telling them that Scully's would-be assassin was killed in a car explosion which destroyed the tape too. Mulder confronts his mother, who tells him that his father was forced to choose whether he or Samantha would be taken. At FBI headquarters Skinner once again meets with the Cigarette Smoking Man about the tape. The Smoking Man calls Skinner's bluff, knowing he no longer has the tape, but Skinner reveals that Albert and 20 other Navajos have memorized the content of the tape and are ready to reveal it if Mulder or Scully is harmed. Mulder meets with Scully at the hospital, who reveals that her sister died a few hours before. Mulder tells Scully that he still believes that the truth is out there. Scully tells him that she's heard the truth, and now what she wants is the answers.

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