Internal dating: Starts on April 16th 1995, as "Anasazi" ends. Mulder is found the following day (17th) and remains unconscious for three days. Meanwhile, Scully is visited by Frohike on the 18th, certainly. After that it gets a little confused. I've carefully counted days and nights and come up with April 22nd as the most likely date for Bill Mulder's funeral, in the morning, and Melissa's shooting in the evening.
Armed men burst in on Albert and his son, asking where Mulder is. "I want Mulder, and I want those files!" Cancerman shouts.
Scully races to Albert's house, arriving to find everyone bruised and beaten. She rushes to the quarry, finding only a blackened and smoking ruin. "Mulder!" she cries, staring wildly at the red desert landscape, getting no reply.
Driving home, Scully is stopped by men who descend from a helicopter. They take the print-out of the files, but she tells them Mulder had the original.
Back in Washington, the Office of Professional Conduct recommends that Scully take a mandatory leave of absence, without pay. She is also told to make herself available for enquiries into Mulder's whereabouts. "To the best of my knowledge, Agent Mulder is dead," she says.
As she leaves, Skinner follows her. Outside his office, she demands to know who these people are - "They're putting an official stamp on the perpetuation of a lie." She says no-one has any intention of finding the men who poisoned Mulder, killed his father and then killed him. Skinner says he will make sure they do. "With all due respect, sir," she says. "I think you over-estimate your position in the chain of command."
Scully goes to Mulder's office to get the digital tape, which has been fastened to the top of a drawer, but there is only an empty case.
46th Street, New York City. In a gloomy room, the Consortium meet and discuss the problem. Cancerman assures them the problem is under control. The FBI is a small problem, he says, but "we'll handle that internally, as usual." One man mentions "the Mulder problem," but Cancerman says he's dead, and the tape has been recovered,
Scully shows up on her mother's door at night, her shoes in her hands. "Oh Mom," she says, crying in her mother's arms. "I've made a terrible mistake. Dad would be so ashamed of me."
In New Mexico, some boys see buzzards in the quarry. The birds, who feed on the dead or dying, lead them to find Mulder, who's collapsed in a tunnel which leads from the boxcar - the same place Albert once found an alien body. Mulder's close to death, so they take him to a hogan and launch into a ritual - the Blessing Way chant.
Scully is awakened by a knock at the door. It's Frohike, clutching an empty bottle, and she invites him in. "He was a good friend," he says, of Mulder. "A redwood among mere sprouts.... I guess this means he's passing you the torch." "I'm afraid not," she says. "I'm soon to be out of a job." He shows her a newspaper clipping about the murder of Kenneth Soona. It's dated the day before yesterday - after Mulder disappeared. "How could they be so stupid?" Scully says.
Performing the Blessing Way ritual, Albert is worried that Mulder will choose death, as his body longs only for rest. Whether he survives or not comes down to whether his desire to live is strong enough. Mulder appears to leave his body and floats in the stars. Deep Throat speaks to him, calling him "old friend," and urging him to feel the fire of intensity that still lives in him. "Go back," he says. "Do not look into the abyss or let the abyss look into you. Awaken the sleep of reason and fight the monsters within and without."
Mulder then sees a vision of screaming alien figures trying to escape cyanide gas in the box car. They are pressing to get out of a tunnel in the side (presumably the way Mulder escaped), but are dying in piles around it.
Bill Mulder comes next, saying he never again wanted to "broker fate with a life to which I gave life. The lies I told you are a pox and poison to my soul, and now you're here because of them. Lies I thought would bury for ever the truth I could not live with. I stand here ashamed of the choices I made so long ago, when you were just a boy. You are the memory, Fox. It lives in you. If you were to die now, the truth would die and only the lies survive us." Mulder asks is his sister is here too, but his father says she isn't. "The thing that would destroy me - the truth I thought you must never learn - is the truth you will find, if you are to go forward," he says, vanishing.
Scully goes through the visitors' entrance to the FBI HQ, setting off the metal detector as she goes in. She goes to see Skinner, telling him about Kenneth Soona's death. She wants him to check the ballistics data on Soona and see if it matches the gun that killed Bill Mulder, in order to clear Mulder's name. Skinner dismisses her idea. She wants him to double-check, but he says, "Miss Scully, I think you underestimate the duties and responsibilities of my position as Assistant Director." He then tells her he had to execute a search warrant on her apartment, and asks about the digital tape. "Is this tape what Agent Mulder died for?" he asks, and tells her to bring him to tape, or else just go home and let them handle it.
After she's gone, Cancerman comes out of hiding. Skinner says she hasn't got the tape. "Is that what she says?" Cancerman asks. "Yes. That's what she says," Skinner replies, none too pleased. "Well, that's unfortunate for everyone," says Cancerman.
Leaving the building, Scully asks to go through the metal detector again. It beeps again, the problem is traced to the back of her neck.
An X-ray reveals a small piece of metal in her neck. She gets a doctor to remove it.
After three days, Mulder awakens and asks for water. "Like a rising sun, I sensed in him a rebirth," says Albert. "Still, it will take time to regain his strength."
A thing removed from Scully's neck looks like a small computer chip. She confides in her sister, Melissa, who says she has to find out what it is. She wants Scully to go through with hypnotic regression to find the buried memories, but Scully is very hostile to the idea. "What are you so afraid of, Dana?" Melissa asks. "Are you afraid that you might actually learn something about yourself? I mean, you are so shut off to the possibility there could be any other explanation apart from your rigid scientific view of the world. It's like you've lost all touch with your own intuition. You're carrying so much grief and fear that you can't see - you've built up these walls around your true feelings and the memory of what really happened."
Scully goes to see Dr Mark Pomerantz, who begins to regress her. He takes her back to her disappearance, asking her what she felt. "I was afraid," she says. (The doctor's questions have been edited out from the next few lines) "...that I would die... There were men. A man took me. There was a light, and... loud sounds my... my ears were pounding... There was an alarm... They wanted to know I was alright... I was powerless. I could not resist them." He then touches her and she pulls out of the trance. "I don't think we're getting anywhere," she says, leaving the room.
Scully pulls up in front of her home and notices Skinner leaving.
In the hogan, the boys give Mulder sunflower seeds, which he asked for in his fever. "In my fever," Mulder says, "I left here and travelled to a place." "This place," says Albert. "You carry it with you. It is inside of you. It is the origin place." "It wasn't a dream?" Mulder asks him. "Yes," Albert replies, enigmatically, and destroys the ritual sand painting.
Scully calls Skinner to ask why he was at her apartment, but he denies he was there. Cancerman is the room.
Mulder appears to Scully in a dream. "I have been on the bridge that spans two worlds - the link between all souls by which we cross into our own true nature," he tells her. "You were here today, looking for a truth that was taken from you - a truth that was never to be spoken but which now binds us together in dangerous purpose. I have returned from the dead to continue with you, but I fear that this danger is now close at hand, and I may be too late." Scully awakens with a start.
Scully goes to Bill Mulder's funeral. She introduces herself to his mother, and tells her she feels Fox is still alive. "I just have a very strong feeling," she says. Well-Manicured Man then introduces himself, calling himself a friend of the family, and a member of a "kind of Consortium. We represent certain global interests". He warns her that she is in danger. They'll either send two men to kill her in her home, or will send someone she trusts who'll arrange a meeting. They'll kill her because she wants "something they don't - justice." He's warning her as he thinks her death will draw unnecessary attention. "Motives are rarely unselfish," he says. She asks what business he's in. "We predict the future," he says. "The best way to predict the future is to invent it."
Mrs Mulder gets home and finds Fox there waiting. "I need your help, Mom. I don't have much time.... I need you to remember." He shows her a photograph of his father with some men. Deep Throat, Cancerman and Well-Manicured Man are visible. He wants to know who they are, but his mother says she doesn't know. "Don't do this to me," she says, when he shouts at her, and asks him what it's all about. He says he thinks it has to do with Samantha.
Melissa calls Scully, saying she'll come round. Immediately after, there's another call which is silent. Remembering the warning, she calls Melissa back, getting no answer, then leaves the apartment, planning to go to Melissa's instead. Skinner drives up and says he has something very important to tell her, and he'll drive her to her sister's afterwards. She gets in the car. She takes him to Mulder's apartment, then holds him at gun point. "I want to know who sent you - whose errand boy you are," she says. "You have the rest of your life to give me answers."
Melissa lets herself into Scully's apartment and is shot by two men - Krycek and Hispanic Man - who are waiting in the dark.
Scully is still holding Skinner at gun point. "How high does it go, Skinner?" she asks. "Who's pulling the strings?" He says she'll spend her life in prison if she kills him, and that would only be doing their job for them. He said he came here to give her the digital tape which he took from Mulder's desk.
Suddenly, footsteps sound at the door. Scully is temporarily distracted, and Skinner takes the opportunity to pull out his own gun.
To be continued in Paper Clip.
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