Episode written by Chris Carter and Frank Spotnitz
Summary written by Diana Williams

TEASER:
Scenes from past shows develop the mythology to date: "Erlenmeyer Flask" - Scully pulls out the alien tissue in cold storage. Nisei / 731 - Scully walks through a train car and realizes that she was in one of these cars before, that this is where they put the implant in her neck. Mulder surveys rows of hybrids in growth tanks. "Red and the Black" - Scully meets Cassandra Spender, Jeffrey Spender learns that CSM is his father, and Krycek tells Mulder about the war raging between the aliens. The Consortium learns about the faceless Rebels, that their facial scarring is to protect them from infection by the black oil. Cassandra Spender tells Scully that they will be calling her soon. Cassandra floats out of her wheelchair up into the sky.
Interior of a train cars: several masked and garbed doctors are working on a patient, checking monitors. One of them makes an incision along the patient's abdomen and green fluid bubbles out. Amazingly, the incision begins to heal itself, leaving only drops of green fluid behind. The doctors exchange looks.
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POTOMIC YARD
ARLINGTON, VIRGINIA
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A train yard at night, with a van sitting beside a train car. A car drives up and Dr. Openshaw gets out. He walks over to the train and one of the garbed doctors comes out. He greets Dr. Openshaw and congratulates him, telling him that his work is complete. The other doctors come out as well. Dr. Openshaw and the first surgeon go into the train car and stand beside the patient. "25 years," the doctor says. "She must seem like an old friend." Dr. Openshaw agrees and picks up the woman's hand. The doctor says that they are going out to celebrate and invites Dr. Openshaw to come with them. Dr. Openshaw turns down the invitation. The doctor leaves him and, as he exits from the train car, he hears a noise behind him. He turns and sees a man behind him. The man, whose mouth and eyes are sewn shut, ignites the doctor and he falls to the ground, bursting into flames. The other doctors waiting in the van stare in horror, then the flame-thrower is stuck into the van and ignited.
Inside the train, Dr. Openshaw is preparing to inject the patient with a syringe when the Rebel Alien enters and knocks him down. As Dr. Openshaw looks up from the floor in horror, the Rebel sets him on fire. The Rebel then turns to the patient and, as his eyes move up her body, we see that it is Cassandra Spender.
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OPENING CREDITS
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The Cigarette Smoking Man lights a cigarette and says, "This is the end. I never thought I'd hear myself say those words after all these years." He is talking to someone that we don't see, telling the person what happened. "We had a perfect conspiracy with an alien race, aliens who were coming to reclaim this planet and destroy all human life. Our job was to secretly prepare the way for their invasion, to create for them a slave race of alien/human hybrids. They were good plans, right plans, kept secret for over 50 years, ever since the crash at Roswell. Kept secret from men like Fox Mulder. Plans that would have worked had not a rebel alien race come to destroy them. Had not my own son chosen betrayal, or chosen to betray more wisely�"
Scene shifts to the X-Files office where Agent Spender is working. A.D. Skinner enters and Spender tells him that he didn't hear him coming, that he was working.
Skinner: Working on what, Agent Spender?
Spender: A progress report on the X-Files.
Skinner: Progress report to who?
Spender: It's just a file.
Skinner: I wasn't aware that you made any progress. In the months since your assignment I've received one memorandum. Were you planning to hit me all at once?
Spender: It's been slow going.
Skinner: The truth is your purpose here is not to make any progress, isn't it? The truth is you have no interest in the X-Files. Beyond a certain personal case. Your mother's abduction.
Spender: Alleged abduction.
Skinner: That's what I'm here about.
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A car drives up to the train yard, and Spender and Skinner get out. FBI agents are processing the scene. They go into the train car and look around. Skinner tells him that a group of men were burned alive, that one is on life support, and that only his mother survived. She is being treated outside. Spender goes to his mother and asks what happened to her, where she's been and she looks frightened. She tells him that she needs to talk to Agent Mulder. Skinner turns and walks away, and Spender hurries after him. Spender says that he doesn't want Mulder to talk to her, that Mulder is forbidden from the X-Files. Skinner asks if he is afraid of the truth, and Spender says that he wants to know who did this to his mother and why, and that's all. Skinner asks why he doesn't use all the resources available to him. Spender tells Skinner he'll send him a progress report.
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CSM continues his narrative, stating that his son still couldn't believe that his mother had been abducted,that Spender couldn't bring himself to accept the possibility of alien life. "When he did come to believe, when the facts became so glaring, he turned � not to me, his father � but to the man I drew him to, the man I'd chosen for him to replace."
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Cut to an indoor basketball court where Mulder and others are playing a game. Mulder looks up when Scully walks in, turns and sinks a basket, then walks over to Scully. She comments that he's obviously not coming into work, tells him that someone wants him back at the office about an X-File.
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FBI Headquarters
Washington, D.C.
Mulder finds Spender sitting at his desk, writing him a note. Spender says that his mother wants to talk to Mulder, tells Mulder that he just wants the truth. Mulder tells him that the truth is out there, and that maybe he should find the truth for himself.
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St. Mark's Medical Center
Arlington, Virginia
CSM enters Dr. Openshaw's room and stands looking down at the doctor who is lying in a hyperbaric chamber. Openshaw tells him that he expected him sooner, and CSM tells him he's been at the trainyard trying to tidy things up. Openshaw tells him that Cassandra is a success. CSM looks stunned. Openshaw tells him that he prepared a syringe but that the Rebel came. CSM says that they saved her to expose the Consortium. Openshaw says that they will run medical tests, that it's only a matter of time, and that Cassandra must be terminated. Openshaw adds that they'll be coming to question him, and CSM says that he knows. Looking genuinely regretful, he says that he's sorry and then turns a knob on the chamber.
Openshaw: A man should never live long enough to see his children � or his work � destroyed.
Openshaw closes his eyes and CSM stares down at him.
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SILVER SPRINGS, MARYLAND
Inside a large house, a phone rings and the Second Elder answers it. CSM tells him what happened while, outside the window, a car drives up and a man gets out. CSM tells the Elder that Openshaw is dead, that he has called an emergency meeting of the Syndicate. The Second Elder tells CSM that he'll be on a plane. The doorbell rings and he answers the door, is stunned to see Dr. Openshaw. He claws at the man's face and it is one of the Rebels. The Rebel grabs the Second Elder by the throat, and then we hear screams and see flames from outside the window.
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9:42 PM
In the darkened Bullpen, an agent is packing up his briefcase while Mulder sits at his desk, looking at pictures from the train yard on his computer. Scully enters and says she didn't expect to see him there. He asks where she expected to find him, and she says that she thought Agent Spender offered him an X-File assignment. Mulder tells her that it wasn't offered exactly, that it's a setup to come down on him full-force. Scully moves around to take a look at the computer and looks at the pictures of the burn victims. She tells him that she's seen it before and he nods. She says that she was with Cassandra Spender when she disappeared, that he sat with her when she was under hypnosis. Mulder says that he doesn't doubt that Cassandra could expose more than what happened to her. Scully questions whether Cassandra could help expose who did this to Scully, and that Agent Spender doesn't have to know.
In the hospital, Cassandra is eating green Jell-O when Scully enters and tells the person guarding Cassandra that they are old friends, showing her badge. Scully asks if she'd like to grab a wheelchair and go out for some fresh air. Cassandra shows her that she can walk now, and says that she's dying for a cigarette. Scully walks down the hallway with Cassandra while the other agent follows at a discreet distance. Cassandra says that she's not going to tell anyone about what happened, only Agent Mulder. Scully smiles and says that she's got a surprise for her. Cassandra enters a darkened room and calls out for Mulder, hugs him, and he is amazed that she is walking, that he had doubts when they last spoke. Cassandra says that he was doubting himself, that he doubted he'd ever see his sister again.
Scully tells Cassandra that Mulder believed he saw his sister last year, but Cassandra tells him that it wasn't her. She says that his sister is out there with them, the aliens. Scully says that Cassandra was found in a train car, that she had been operated on, and Cassandra says that she was cured by the aliens, that the doctors were working with them. She says that she told them last year that the aliens were here to do good, and that she was an oracle to spread the word. Only now she knows what the aliens are here for: to wipe us off the planet. They are taking over the universe, infecting other life forms with a black substance called "purity", their life force. Mulder comments that it's the virus, the black oil. Scully says that the doctors were burned, not infected. Cassandra says that they were burned by another race of aliens, Rebel forces that are mutilating their faces so they won't be infected. She says that this is what she couldn't tell her son, that he wouldn't believe her, even though his life is danger from them. She tells them that he's in with the men that have been working with the alien colonists. Scully asks "working to do what?" and Cassandra replies, "whatever it is they did to me, and to you, Dana."
Mulder asks is she knows who the men are and she says that one of them is her ex-husband, Jeffrey's father.
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CSM continues talking, saying that Cassandra was beginning to realize her role in the greatest science project that man had ever known, that she was the center of 50 years of work, the key to all their plans. "I killed to keep them [my colleagues] unknowing. I killed Dr. Openshaw so they wouldn't discover her, when it's Cassandra I should have killed. Cassandra who needed to die. I couldn't do it. With all the blood on my hands, I couldn't kill the mother of my own son, a woman I never even loved." He says that his colleagues never knew, that they were focused on the new threat, the faceless alien rebels.
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At a gathering of the Syndicate, Krycek tells them that rebels have attacked and burned project facilities in New Mexico and the southWest. The medical staff at the Arizona research facility have been slain. Work on the alien/human hybrids will suffer from the death of Dr. Openshaw. Members of the Syndicate wonder what the Rebels want, and CSM says that they want to expose their enterprise. Another worries that a reporter or law enforcement will put the pieces together. CSM comments that their new man at the FBI is very capable of diverting attention. One of the members says, "Why not side with the rebels, join their alien resistance." And we see that it is the Second Elder, the man that the rebel killed earlier.
Krycek: It is an option you declined long ago. Resistance was futile then, why would it be any less so now? That's why you voted against it, against men like Bill Mulder. Collaboration has allowed you to prepare, to stall colonization. How close are you to develop an alien/human hybrid? That alone ensures your survival.
The Second Elder/Rebel Impostor comments "as slave labor for the aliens" and Krycek reminds them of the vaccine. CSM comments that they've worked on this for 50 years, that they can't sacrifice themselves for every new threat.
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Mulder and Scully enter the X-Files office and Scully asks why are they risking getting caught here. Mulder tells her that they'll be monitoring their machines. He searches for Spender in the database and finds that CSM is listed as C.G.B. Spender, Cassandra Spender's ex-husband, but there is no information available.
Skinner enters and tells them to get up, shut down the computer, and get out � that "they" are coming. Mulder asks who, but Skinner just rushes them out. Spender comes down the hallway with three agents behind him.
Spender: Assistant Director. I'll assume that you came down to apprehend these agents for unauthorized entry to my office. I'll make sure that it's duly noted in the report of their dismissal.
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Spender enters a room where CSM sits smoking and tells him that he's done as he asked, that Mulder and Scully will be processed out of the FBI. He wants CSM to do something for him. He wants the truth about his mother. CSM says he won't believe his mother, won't believe him. Spender tells him that he needs to know. CSM says that he needs to show that he's capable of handling the responsibility that comes with this knowledge. Spender says, "Don't try me, old man." CSM slaps him and tells him that he gave him responsibility, a position, things that he couldn't get himself and he couldn't do the job. Spender says that keeping Fox Mulder down is not a job, it is CSM's dirty work. CSM slaps him again and Spender staggers into a chair. CSM compares him unfavorable against Fox Mulder.
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Back at the basketball court, Mulder is shooting baskets and Scully enters with a file box. She tells him that she is curious about C.G.B. Spender, that it appears to be an alias. She asks if he's curious about what's in the box, and he says that nothing she could ever find will be accurate or credible. She says that there is a picture he's going to want to see. It is of CSM and his father, taken in 1973, linked to a project they worked on for 25 years at the State department. She shows him Cassandra's file, that she was first abducted on Nov 27, 1973, the same night as his sister. There are other names connected to C.G.B. Spender and Bill Mulder, including Openshaw.
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CSM continues, saying that Mulder now was fueled with names and dates and certainties. He couldn't stop him any further, stop him from learning the sins of himself and Mulder's father. But he had one last chance to preserve his legacy.
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DOWNTOWN WASHINGTON
7:10 PM
Spender stands on a street corner as a car drives up and CSM gets out. CSM says that he has a new job for him, that he has been unduly harsh and that Spender deserves a fighting chance to prove his father wrong. He hands him one of the ice pick type devices, tells him that it is a weapon. CSM tells his son that a man has infiltrated the group, disguising himself as a man that he has already killed. He tells Spender to greet him as that man, engage him in conversation, and put the pick in the back of the man's neck. He opens the car door and reassures his son that he can do it. Spender gets in the car, and we see that Krycek is the driver. He says to watch where Spender points the pick, and they drive off.
They arrive outside the Silver Springs house and Spender goes to the door, ringing the doorbell. He introduces himself to the Second Elder and says that his father sent him to see him, that he has a message from the group. The Elder asks if they have changed their minds, and Spender says that's what he's here to talk about. They sit down and Spender says that he has a name, one that will have meaning for the Elder. He drops the card with the name and the Elder bends over to pick it up. Spender hesitates, then raises the pick, but he's been too slow and the Rebel Impostor grabs him by the hand and neck. Spender struggles, scrapes off the Rebel's face and freaks. Krycek comes up behind the Rebel and stabs him in the base of the neck with the weapon. The Rebel collapses, oozing green, and Spender stares at Krycek, stunned.
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Mulder opens his apartment door and thanks Skinner for coming over. Scully is inside and they tell him that Cassandra Spender's life is in danger. Skinner asks who she's in danger from and Mulder says from men who have conducted medical experiments to develop alien/human hybrids that will survive the viral apocalypse when the aliens colonize the earth. Skinner asks about proof, and Mulder says that Scully has dug up files that make all the right connections: to Dr. Openshaw, to his sister, to his father, to Agent Spender's father � the smoking man. Skinner is stunned and Scully confirms it. He asks if Scully believes it, and Mulder says that she has her doubts about the purposes but that she believes she was a test subject. Skinner says that if Cassandra Spender's life is in danger, why not Scully's life? Mulder says that he believes that Cassandra is the first successful alien/human hybrid. Skinner asks why her life would be threatened. Mulder says that the men that created her would rather kill her than let her expose their enterprise. Skinner says that she's under 24 hour guard, and Mulder points out that they are assigned by Agent Spender.
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At the house in Silver Springs, Spender watches the dissolving alien corpse. Krycek re-enters the room
Krycek: You've never seen one before, have you? It's shocking at first. The acceptance of the idea � it's something you thought only children and fools believed it. It undermines your beliefs - in yourself, in the world. But then you come to understand.
Spender: Understand what?
Krycek: Well, the responsibility this knowledge demands of the men who have it. The great sacrifice by great men � like your father.
Spender: What sacrifice?
Krycek: The sacrifice of your mother.
Spender (stands up): What do you know about that?
Krycek: Just � she's been the subject of an experiment for 25 years.
Spender: My father's involved in that? Is he?
Krycek: Your father directs the experiments.
Spender: So I'm protecting her now so the experiments can continue?
Krycek: That's why he put you in the X-Files. That's why your father sent you here tonight. You're protecting the project, Jeff. Making the sacrifices. So that you can be a great man, too.
Spender: I'll be my own man.
He walks out.
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CSM continues talking, saying that he trusted no one, that treachery is the result of all favors. "I have little doubt of my son's disloyalty to me. Certainly he led Mulder and Scully to us. His mother must know by now her central role in the grand plan, that she's as much alien as human. Do you wonder why I've chosen you? You've never betrayed me. Now I need someone to trust."
Diana Fowley stands up and tells him that she'll help him, that it's not too late. She circles around his chair, trailing an arm over his shoulder, and leaves the room.
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Skinner enters the hospital and sees that the guard is missing outside Cassandra Spender's room, that Cassandra herself is missing. Spender arrives and asks where his mother is. Skinner tells him that she was gone when he got there. Spender tells him that "he" took her and goes to the phone while Skinner asks "who?"
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There is desperate pounding on Mulder's door, and he opens it to find Cassandra on the other side. She is panicked and tells them that they can't let "them" find her. There is more pounding on the door. She tries to grab Mulder's gun and tells Mulder that he has to kill her, that if he doesn't kill her, it all starts and there won't be any stopping it. She begs Mulder to shoot her, and he raises his gun, pointing it at Cassandra Spender. Scully insists that they have to protect her, and Mulder tells Scully to stand away. Mulder and Cassandra lock eyes down the barrel of the gun, Cassandra looking hopeful and Mulder looking pained�
TO BE CONTINUED