(A barbed wire gate with barbed wire on top is locked with a chainlock. That does not stop the massive army trucks, who drive through the gate and continue into the Hansen's Disease Research Facility. The trucks stop and troops unload.)

SOLDIER: Come on, let's go. Move, move!

(Under a small trap door in the floor, someone watches as the troops make certain strange-looking men file outside.)

Move! Let's go. Outside.

MAN #1: Move it, move it, move it.

SOLDIER: Go! Let's go.

(Babies start to cry as dozens of these poor men come out of the dark recesses of the room.)

Come on, come on. Let's go, let's go!

MAN #1: Let's go! You, move it, come on!

SOLDIER: Outside, everybody outside. Hurry, hurry! Let's go!

(As they leave, the head soldiers closes the curtain and the sounds fade to a din. A man runs out of the trap door and looks out the windows as the soldiers move the hybrids into the trucks.)

Come on, get in, get in.

MAN #1: Hurry up!

SOLDIER: Let's go, let's go.

MAN #1: You, hold it, get up, get up!

MAN #2: Get them moving. Fast, fast, fast, come on.

MAN #1: All the way in the back! It's clear!

(The driver starts the truck and they drive off. The strange man, Escalante, runs after them, trying to see what is going on.)

MAN #2: Fan out!

SOLDIER: All right, let's get everyone.

(The strange creatures form a line in front of a giant trench as Escalante watches. He has Hansen's disease, commonly known as leprosy.)

MAN #1: Turn around, face forward! Turn around and face the other way! Now!

SOLDIER: Fire!

(The soldiers, lined up, fire into the line of people. Escalante averts his eyes from the mayhem. Ceasing fire, the troops walk up to the trench, look in, and go back to their trucks.)

(Scully is talking to Mulder on the phone, her manner urgent. X watches her.)

SCULLY: Mulder? Answer me!

(Cut to Mulder, who lands harshly on the roof of the boxcar, dropping his phone. He reaches for it as it slides off the side of the train.)

MULDER: Aw, damn it.

(Looking around as the train moves, he slowly stands and, balancing himself, makes his way along the top of the train. Cut back to Scully, who hangs up and looks at X.)

SCULLY: I want to know what's on that train.

X: It doesn't matter now.

SCULLY: Our government is operating a secret railroad. They put something on that train in West Virginia, something living.

X: What more is there to know?

SCULLY: What the Japanese have to do with it. How a man named Ishimaru is involved.

X: That I don't know.

(He turns to leave. Scully pulls out her gun.)

SCULLY: Don't tell me you don't know, you smug son of a b...

(He grabs the gun from her, too fast for her to react. She looks at him in shock.)

X: There are limits to my knowledge.

SCULLY: I don't have time for your convenient ignorance.

X: What were you going to do? Shoot me? Just like the men that shot your sister?

SCULLY: You know them too?

X: You want to know what's on that train? Who killed your sister? You find out what they put in your neck.

SCULLY: The implant.

X: It holds more than I could ever tell you. Maybe everything you need to know.

(She looks away, thinking. He holds her gun handle out to her and she takes the gun back. He then walks out.)

(Darkness has fallen. Mulder climbs down a ladder on the side of one of the cars and in through a door. As he walks in, he notices a door marked "quarantine" with a keypad with red glowing buttons. He tries the door, but it is locked. Looking at the keypad, he then looks back through the window and walks into the main hallway. He spots a conductor making his way down the hall and goes over to him.)

MULDER: Excuse me. I need your assistance. I'm a federal agent, my name is Mulder.

(He shows him the badge.)

CONDUCTOR: You need my assistance?

MULDER: I need access to that quarantine car you picked up in West Virginia.

CONDUCTOR: Sorry, can't help you.

MULDER: I'm a federal agent, sir. I need you to open that car.

CONDUCTOR: I would if I could, but I don't have access myself. We pick these cars up from time to time. Whatever they're carrying, they never let us know.

MULDER: Well, somebody's got to be able to get in that car.

CONDUCTOR: We've got a doctor on board, came on back at Queensgate. He might have something to do with that, I saw him back there, checking the door.

MULDER: What's his name?

(The conductor looks at a list of passengers.)

CONDUCTOR: Japanese fellow, Doctor... Shiro Zama. Traveling with another party, it says, but I got the impression he was alone.

MULDER: Can you take me to his compartment?

CONDUCTOR: Certainly. Right this way.

(Mulder follows the conductor to a hallway with many doors. He points to one as Mulder draws his gun.)

MULDER: Stay here. Knock on the door but stay away from it.

(They stand on either side of the door. The conductor knocks.)

CONDUCTOR: Doctor Zama?

(They wait for a second, but receive no answer.)

MULDER: Knock again.

(The conductor does so.)

CONDUCTOR: It's the conductor, Doctor Zama.

(A bell sounds in the back. No answer is given again.)

MULDER: Open it. Just unlock it and step away.

(The conductor takes out his keys and unlocks the door. Mulder looks around then pushes open the door and points his gun, searching the compartment. No one is there. As the conductor peeks in, Mulder opens Zama's briefcase and looks through a notebook with notes in Japanese.)

Why did I study French in high school?

(He closes it up.)

You got a safe place you can put this?

CONDUCTOR: Yes.

(Mulder hands him the briefcase.)

What am I supposed to tell the doctor when he asks where it is?

MULDER: If he finds you before I find him...

(He bends down and pulls out another gun strapped to his ankle.)

I want you to make him lie on the ground till I get back, okay? You understand?

(The conductor stares at him.)

Have you ever used a gun before?

CONDUCTOR: No.

(Mulder takes the clip out.)

MULDER: I just want you to point it at him.

(He demonstrates how the gun is empty.)

Don't pull the trigger. That will kind of give away the game.

(The conductor chuckles. Mulder hands him the gun.)

CONDUCTOR: What if he runs?

MULDER: Just make sure he runs my way.

(Mulder walks down the hallway.)

(Scully sits with Agent Pendrell, who has the chip hooked up to various machines. He looks through a microscope as he pumps charges through it, Scully sitting at the desk, looking at the monitor. A read-out of the electronic impulses is on the screen.)

PENDRELL: I'm feeding the chip impulses. The graph is recording its output, which, when I remove the current, changes slightly but continues. This means the neural network is storing information.

SCULLY: Biological information?

PENDRELL: That was my first guess. You've already told me the chip was placed subcutaneous under the back of the neck, right?

(She nods.)

So it makes sense that it would be recording impulses traveling to and from the central nervous system.

SCULLY: But what?

PENDRELL: But look at the graph. Those are what we call reverbatory loops. They indicate the presence of circular neuronal activity in the brain.

SCULLY: Memory formation.

(Pendrell nods.)

PENDRELL: Yeah, the chip seems to be mimicking that process, replicating the memory process in the brain.

SCULLY: Like a computer hard drive.

PENDRELL: Yeah, but no hard drive we've ever seen. This kind of neural network could be not only collecting information, but artificially replicating a person's mental processes.

SCULLY: You could know a person's every thought.

PENDRELL: Frightening.

(Scully looks away and gasps slightly, covering her mouth. She arches her eyebrows and nods. Pendrell stands and starts around the table. She follows.)

Anyway, I showed the chip to some of my techheads and they weren't as blown away as I thought they'd be.

SCULLY: They've seen this technology before?

(He walks over to a desk and turns on a lamp.)

PENDRELL: Well, they've seen neural nets before, but never one as complex as that... nor are they likely to anytime soon.

SCULLY: What do you mean?

PENDRELL: The chip's so delicate that I effectively destroyed it when I began working on it... but I found something in the silicon matrix, what I believe is the name of the manufacturer.

SCULLY: It's Japanese, isn't it?

PENDRELL: How'd you know?

SCULLY: Oh, it was just a guess.

PENDRELL: Well, I checked for you. I assumed you'd want me to... but there's no record or information on the manufacturer either here or in Japan, except this.

(HE HANDS HER A SHEET THAT READS:

"NOT APPLICABLE NOT APPLICABLE
DR. SHIRO ZAMA (304) 555-0103
R.R. 214
PERKEY, WEST VIRGINIA
26301")

I had Fed Ex, U.P.S., the postal service... every commercial courier go through their computer records. They turned up one shipment, sent to a Doctor Shiro Zama at a research facility out in Perkey, West Virginia.

SCULLY: Well done, Agent Pendrell. Keep up the good work.

(She pats him on the arm.)

PENDRELL: Hey, thanks. Keep it up yourself.

(She looks at him strangely, then takes her coat and leaves. He sighs.)

"Keep it up yourself." What a doof.

(The train blares its horn as it speeds down the tracks. As Doctor Shiro Zama makes his way down a car, a certain Red-Haired Man watches him carefully. Zama goes into the next car and the Red-Haired Man slowly follows. Zama looks behind and sees the man following him. He goes into the bathroom but the Red-Haired Man runs up and holds the door open, then swings it open. He takes out two silver bars with a connecting cord as Zama cowers in the stall.)

SHIRO ZAMA: Please...

(The door closes as Mulder walks down the hallway past the room. The bathroom label changes from "vacant" to "in order.")

(Scully pulls up to the installation and gets out, holding her flashlight. She hears a bang and spins around to see a man running by.)

SCULLY: Hey!

(Hearing many footsteps, she then manages to see two men running into a building. She follows.)

Stop!

(She runs up the stairs into the building. The only sound is her footsteps as she walks through the vacant room. She feels a lamp on the desk and gasps at it still being hot. Hearing a creak, she turns around to see another man shrink down into a trap door. She slowly makes her way over to it. Pulling up the small cord, she looks into the hole and sees many men with the same skin condition as the man had before, all cowering in fear of Scully.)

ESCALANTE: Please... don't... don't hurt us. Please? Don't...

(She stares at the leper community below her.)

(Mulder makes his way down another passenger car, looking at the various people in the seats. There is a murmuring amongst the crowd that fades as he moves to the next car. He sees the bathroom door ajar, although the "in service" sign is still on.)

MULDER: Excuse me?

(He pushes open the door to see Zama on the floor, dead. A woman screams behind Mulder.)

MOTHER: Oh, oh, God, he's dead.

MULDER: No, no, shh shh shh, he's just got a little motion sickness.

(He walks over to her and closes the door behind him. She holds her son.)

I'm going to go find a doctor. Why don't you and the young man just find another bathroom?

(He smiles and rubs the kid's head. They walk away. Mulder slides open the door slightly, looks in, then closes it.)

(The strange lepers seem to be afraid of the light.)

SCULLY: Who are you? Don't worry. I'm not going to hurt you. I'm an FBI agent.

(She shows them her badge.)

ESCALANTE: We, we live here. We've lived here at the facility most of our lives.

SCULLY: What kind of facility?

ESCALANTE: The Hansen's Disease Research Facility.

SCULLY: Hansen's Dis... do you mean this is a leper colony?

ESCALANTE: No more, they... the facility's closed now.

(She looks around at the disfigured outcasts.)

SCULLY: L, look. I, I, I came here looking for a Doctor Shiro Zama.

ESCALANTE: Doctor Zama... isn't here anymore. None of the medical staff is.

SCULLY: Where did they go?

ESCALANTE: Well... they all left right before the death squads started coming.

SCULLY: What death squads?

ESCALANTE: That's, that's who we've been hiding from. We thought you'd come to kill us... like they killed all the others.

(She stares at him. Later, he leads her through the woods.)

SCULLY: How many have been killed?

ESCALANTE: Hundreds. All but us.

SCULLY: I don't understand how there could have been hundreds of people here when, when leprosy is supposed to be a treatable disease.

ESCALANTE: Well, it is. Me... and, and, and the other people back at the hiding place? We're the last. Our disfigurement forced us into the camps before there was a treatment.

SCULLY: Who were the others?

ESCALANTE: We never knew. They began arriving several years ago but they were kept apart from us.

SCULLY: And they had Hansen's disease?

ESCALANTE: No, no, they had the Hansen's deformities. Doctor Zama would... round them up in groups for treatment. And then the, the ones that returned always came back worse.

(They stop.)

With terrible burns all over their bodies. It's over there.

(He starts off again, and she follows quickly. They walk over to a trench and Scully gasps in horror at the hundreds of bodies piled on top of each other, each with the alien features.)

SCULLY: Oh, my God... oh...

ESCALANTE: There are more of these pits. They just... dump the bodies on top of each other... like they were garbage.

(A helicopter approaches.)

They're coming!

(He starts off.)

SCULLY: Wait! Hey!

(He stops as the helicopter's searchlight shines through the trees and into the clearing they are in.)

ESCALANTE: No...

(He runs off. Scully tries to shield her eyes from the blinding light shining down upon them. Escalante looks back briefly and Scully follows. The searchlight stays on them as they go through the forest. People with red flashlights approach in front of her. She gasps and turns around only to see more jump out in front of her, led by the same one as before.)

SOLDIER: Move and you're dead.

(Gunshots sound off from behind her and she turns around in horror at the fate of Escalante.)

(Mulder makes his way through another car and into the next one. He walks over to the conductor.)

MULDER: I found Zama four cars up, strangled in the bathroom.

CONDUCTOR: No.

MULDER: Now, I want you to get up there and seal off that bathroom. I want you to get word to the engineer not to stop this train until I tell him, okay? Until I find the killer.

(The conductor nods. Mulder walks off as the conductor heads in the direction Mulder came from. Mulder comes to the same door with the keypad but finds it open. Drawing his gun, he makes his way inside the dark cabin and past the various machines and cabinets over to a dissecting table in the middle. Passing that, he sees a flashlight shining through another door at the end. Looking through, he sees the living being cowering in fear, a flashlight on him. The shape of the non-human being is reflected in Mulder's green eyes. The being walks towards the door as the Red-Haired Man comes up from behind Mulder and grabs him by the neck, then slams his fist into the door, forcing Mulder to drop the gun. Strangling Mulder with the bars and cord, he tosses him into the table like a ragdoll then pushes him down onto the ground. As the Red-Haired Man pulls up on the cords, cutting off the last of Mulder's air, the conductor aims his gun at the villain.)

CONDUCTER: Hey!

(The Red-Haired Man looks up in shock. Mulder slumps down, barely alive. The Red-Haired Man drops the bars and slowly gets to his feet, hands raised.)

RED-HAIRED MAN: I'm a law enforcement officer.

CONDUCTOR: Stay back.

RED-HAIRED MAN: Just put the gun down.

(He straightens his tie as the conductor holds the empty gun trained on him.)

I'm going to show you my identification.

(He reaches into his pocket and pulls out his badge. He walks slowly towards the conductor.)

Put the gun down.

(The conductor runs for the door, the Red-Haired Man giving chase. Before he can grab the conductor, the door is slammed and locked. The conductor peers in from the other side. The Red-Haired Man bangs on the door.)

You idiot!

(As he slams against the door, the conductor runs out of the outside room.)

MULDER: Put your hands in the air and turn around!

(The Red-Haired Man's body tenses.)

Put your hands in the air!

(The Red-Haired Man fixes his tie and faces Mulder, who is standing in the doorway, gun trained on the man. The villain puts his hands up. Mulder holds his neck. The Red-Haired Man slowly approaches him.)

RED-HAIRED MAN: You have no idea what you're dealing with here.

MULDER: Well, maybe you should've filled me in before you tried to kill me. Now, who are you?

RED-HAIRED MAN: No. Who are you?

MULDER: Answer me!

RED-HAIRED MAN: I work for the National Security Agency.

(Mulder starts to laugh a little.)

MULDER: The N.S.A.? Since when did they start issuing you guys piano wire instead of guns?

(The Red-Haired Man points to his inside coat pocket. Mulder watches him carefully as his attacker takes out his badge.)

RED-HAIRED MAN: Since we learned there's a bomb on this train.

MULDER: There's something on this train, but it's not a bomb. Throw that here.

(The Red-Haired Man tosses Mulder his badge.)

RED-HAIRED MAN: This car is wired to an explosive device. It armed automatically when I entered the car.

(Mulder tosses the badge back. The cut on his neck is quite visible.)

MULDER: Why?

RED-HAIRED MAN: Because of what's in that room. Because if the man responsible for it couldn't get it out of the country, he would rather kill it than let it live.

MULDER: So you killed him.

RED-HAIRED MAN: The only humane alternative, given the circumstances.

MULDER: Put your hands in the air.

RED-HAIRED MAN: This bomb could be wired to anything in the car. The slightest concussion could set it off. If you use that weapon, you take your chances.

(He turns around. Mulder breathes in a sort of taunting relief.)

MULDER: I'll take my chances.

(The Red-Haired Man looks at him, astonished.)

(Two soldiers lead Scully into a bunk hall, where the 1st Elder sits on a cot, facing the window.)

1ST ELDER: I'd like to speak with Miss Scully alone.

(The soldiers leave. Scully stares at the back of this man.)

SCULLY: How did you know my name?

1ST ELDER: I know most everything about you, Dana.

SCULLY: What are you talking about?

(The Elder faces him.)

1ST ELDER: I think you know.

SCULLY: Who are you? What is this place?

(The Elder slowly walks over to her, his footsteps echoing.)

1ST ELDER: This was one of the most frightening places on the earth. A place where society sent its monsters to live in shame and isolation. Now, their disease is all but conquered. Science has eliminated thousands of years of misery.

SCULLY: I've seen your methods of elimination. What happened to the man who was with me in the forest? What about the people who were in this room?

1ST ELDER: They had been exposed.

SCULLY: Exposed to what?

1ST ELDER: The same thing all these victims have been exposed to him... victims of an inhuman project run by a man named... Zama.

SCULLY: You mean Ishimaru. You hid him here after the war. He stayed here, and he continued his experiments.

1ST ELDER: The ruler of the world is no longer the country with the bravest soldiers, but the greatest scientists. Unfortunately, Ishimaru began to conduct his work in secret, not sharing with those who had risked much in giving him his asylum.

SCULLY: What was he exposing these people to?

1ST ELDER: Terrible things.

SCULLY: What kinds of things?

(He looks away.)

Have I been exposed?

1ST ELDER: I don't know.

SCULLY: Who knows?

1ST ELDER: Please, I'd like to show you something that will give you your answers.

(He walks past her and holds open the door for her. They walk out.

(The conductor and another man stand outside the door.)

CONDUCTOR: Agent Mulder?

(Mulder looks through the window at the conductor.

Do you want us to try prying this door open?

RED-HAIRED MAN: I wouldn't recommend that.

(Mulder looks at him briefly, gun still trained. He looks back at the conductor.)

MULDER: No.

(Mulder walks towards the Red-Haired Man.)

Where's the keycard?

RED-HAIRED MAN: It's in my pocket.

MULDER: Take it out. Slowly.

(The Red-Haired Man pulls out his keycard slowly.)

Put it on the table.

(The man does so. Mulder picks it up and heads for the keycard pad)

RED-HAIRED MAN: It's not going to work.

MULDER: No? How did you get in here?

(The man glares at Mulder.)

But there's a code, right? Zama gave you a code just before you killed him. What is it?

RED-HAIRED MAN: Four ones, a four-seven and a one.

MULDER: One-one-one-one-four-seven-one.

(Mulder walks over to the keypad.)

RED-HAIRED MAN: I'd assume Zama would be smarter than to give me the entrance and the exit code.

MULDER: What?

RED-HAIRED MAN: He knew he was going to die. When I used the code to enter the car, it activated the bomb. You use it again, it'll almost certainly set it off.

(Mulder slowly approaches him.)

MULDER: There's a bomb on this train, where is it?

RED-HAIRED MAN: I don't know. It could be anywhere.

MULDER: No, it couldn't be anywhere. If you activated it coming in here, it's got to be on this car.

RED-HAIRED MAN: You're probably right.

MULDER: Where do you think it is?

(The man shrugs.)

RED-HAIRED MAN: I don't know.

MULDER: You know what I think? I think you're a liar. I don't think you work for the N.S.A. and I don't think there's a bomb on this train.

(Mulder goes back to the keypad.)

RED-HAIRED MAN: You're choosing a hell of a way to find out!

MULDER: Shut up!

(Mulder slides the keycard through the sensor and pushes four ones, a four, and a seven when a chirping alarm goes off, startling both of them. Mulder tenses up before realizing it is the Red-Haired Man's cellular phone.)

That's you. Answer it.

(He does so, slowly.)

RED-HAIRED MAN: Yes? Yes. Just a moment.

(He extends the phone to Mulder.)

It's for you.

(Mulder smirks.)

MULDER: Put it down.

(The man does so. Mulder picks it up and raises it to his ear.)

Yeah.

(Cut to a white autopsy room much like the one where the video autopsy was conducted.)

1ST ELDER: Mister Mulder, I have someone here who'd like to speak with you.

(He hands the phone to Scully.)

SCULLY: Mulder, it's me.

(Cut to Mulder.)

MULDER: Scully, where are you?

(Cut to Scully.)

SCULLY: I'm in West Virginia.

MULDER: Who dialed this number?

SCULLY: Mulder, we've gotten involved in something, but it's not at all what you think.

(Cut to Mulder.)

MULDER: What are you talking about?

(Cut to Scully.)

SCULLY: Whatever is on that train is not alien.

(Cut to Mulder, who motions for the Red-Haired Man to move away from the door. Mulder approaches it as he does.)

MULDER: You're wrong, Scully.

SCULLY: Mulder, Ishimaru Zama...

(Cut to Scully.)

He was experimenting on innocent human subjects.

(Cut back to Mulder.)

He'd been doing it for years. Operating out of a leper colony.

(Mulder closes off the glass screen door.)

MULDER: Well, whatever his name was, Scully, he's dead. I don't think this has anything to do with lepers.

SCULLY: The leper colony was just a front. The tests weren't just on lepers. They were on the homeless...

(Cut to Scully.)

On, on, on the insane, they were brought here and they were subjected...

(Cut back to Mulder.)

...to diseases and radiation tests.

(Mulder looks through the window at the person inside.)

MULDER: Who told you this?

SCULLY: The man who handed me the phone.

MULDER: Well, why do you believe him?

(Cut back to Scully.)

SCULLY: Because of what he's shown me.

(Cut to Mulder, who looks back at the Red-Haired Man.)

MULDER: What? What's he shown you?

(Cut to Scully, who walks past plastic curtains into a room much like that on the video and in the boxcar. A dissection table sits in the middle. The Elder walks slowly behind.)

SCULLY: Mulder, I'm standing in a train car just like the one in your alien autopsy video... only I realize that I've been here before.

(Cut to Mulder, who keeps his gun trained on the Red-Haired Man, who is still on the other side of the glass.)

MULDER: What are you talking about, Scully?

(Cut back to Scully.)

SCULLY: This is where they brought me, Mulder. This is where they put the implant in my neck, in one of these cars.

MULDER: Scully...

SCULLY: It all makes sense, Mulder. Ishimaru Zama, he was using the secret railroad...

(Cut to Mulder.)

...to conduct his tests across the country. The women in Allentown, they all remember these cars.

(Static builds on the phone Scully talks illegibly, garbled under the static.)

MULDER: Scully? Scully?

SCULLY: Can you hear me?

MULDER: Yeah. So what are you saying, that Zama is the one who abducted these women?

(Cut to Scully.)

SCULLY: What I am saying, Mulder, is that there is no such thing as alien abduction.

(Cut to Mulder, who listens in disbelief.)

It is just a smoke screen, happily created by our government to cover-up the biggest lie of all.

MULDER: What about the UFO I saw them working on?

SCULLY: That wasn't a...

(Cut to Scully.)

...UFO, Mulder. It was a piece of a Russian nuclear sub that was raised. More lies.

(Cut back to Mulder.)

MULDER: How can you be so sure?

(Cut to Scully.)

SCULLY: Because I have what I told you I needed, Mulder... proof. Two weeks ago, the president made a public apology for secret radiation tests that had been conducted on innocent citizens up until 1974.

(Cut back to Mulder.)

Only, guess what?

MULDER: Those tests never ended.

(Cut back to Scully.)

SCULLY: Mulder, listen to me. You have got to stay out of that train car.

(Cut to Mulder.)

MULDER: Why?

(Cut back to Scully.)

SCULLY: Because there is a bomb on board.

(Cut back to Mulder.)

Mulder, if that bomb detonates, thousands of people are going to die of hemorragic fever. That's what the test subject inside has been exposed to.

MULDER: Well, Scully, you're a little late. I'm locked inside that train car.

(He sees the Red-Haired Man walking around and aims his gun again. Cut to Scully, who starts walking.)

SCULLY: Well, then we've got to get you out of there. 'Cause that device is on a timer.

(Cut to Mulder, who opens up the glass door.)

MULDER: Where is it?

SCULLY: There should be...

(Cut back to Scully, who pulls apart some plastic curtains and looks up into a hole in the ceiling.)

...a ventilation grid on the ceiling. It's hidden up inside.

(Cut to Mulder, who looks up at the ceiling, then at the Red-Haired Man.)

MULDER: Step back.

(Mulder looks at a ventilation grid and points to it.)

Open that.

(The Red-Haired Man reaches up. Cut to Scully, who waits, anticipating the worst. Cut back to the Red-Haired Man, who pulls off the vent. After staring at it for a little while, the man puts down the grid.)

SCULLY: Did you find it, Mulder?

MULDER: Hold on.

(Mulder looks up into the duct and sees a bomb. The timer is on 1:42:00 and slowly counting down.)

Oh yeah, I found it.

SCULLY: How much time do you have?

MULDER: Little over an hour and a half.

(Cut back to Scully, who is standing next to the Elder now.)

SCULLY: Look, Mulder, you've got to get them to stop that train so we can get you off of it.

(Cut to Mulder.)

They want you to tell the engineer to stop at the next station.

MULDER: Why?

(Cut to Scully.)

SCULLY: So we can get a bomb squad out there.

(Cut back to Mulder.)

And evacuate the train.

MULDER: Uh, Scully, you're breaking up. I can't hear you.

SCULLY: Did you hear that?

MULDER: Scully?

SCULLY: Mulder?

MULDER: Scully?

SCULLY: Mul...

(Mulder hangs up. Cut to Scully, who hangs up as well.)

1ST ELDER: Where's the next stop?

SCULLY: It's not on the map.

(She hands him the phone and starts out. He follows. Cut to Mulder.)

MULDER: Step aside.

(He moves away and Mulder goes to the door, looking at his previous attacker the whole time.)

Conductor?

(The conductor walks up to the door.)

Where are we?

CONDUCTOR: Iowa. We passed Murray station about twenty minutes ago.

MULDER: All right, listen to me. I want you to get word to the engineer that there's a bomb on this car.

CONDUCTOR: A bomb?

MULDER: That's right. I want you to tell him not to make his next scheduled stop and to reroute, you understand?

CONDUCTOR: I think so.

MULDER: I want you to tell him to choose a place as far away from a populated area as possible and unhook this car.

(The conductor scurries off.)

RED-HAIRED MAN: What are you doing?

MULDER: Let's move into the corner over there, now.

(The Red-Haired Man starts to walk, Mulder standing close behind.)

RED-HAIRED MAN: You're going to get us both killed.

MULDER: I want you to kneel down and put your hands behind you back.

(The Red-Haired Man slowly does so.)

RED-HAIRED MAN: They'll never be able to find us in time.

MULDER: If what's on this train is important as I think it is, they will.

(It is now morning and the trains screeches to a halt. A man walks out and switches the track path. The train moves along, carrying the final car, labeled "82517." Inside, Mulder talks to the man. The Red-Haired Man fidgets. Outside, the man unhooks the car.)

RED-HAIRED MAN: You're going to die, you know that?

(Mulder lowers his gun and walks over.)

MULDER: What do you care? You were trying to kill me anyway.

(Mulder walks back away. The Red-Haired Man notices a scalpel on the floor. The train slowly pulls away, leaving the boxcar behind. The timer on the bomb now reads 01:11:06.3 and ticking down. Mulder looks at his watch.)

(As she is driving down the road, her cellular phone rings. She picks it up.)

SCULLY: Scully.

(Cut to Mulder.)

MULDER: Scully, let me tell you, you haven't seen America till you've seen it from a train.

(Cut to Scully.)

SCULLY: Damn it, Mulder, what happened?

(Cut back to Mulder.)

MULDER: We're not going to make that station, Scully.

(Cut to Scully.)

SCULLY: Yeah, I figured that, do you have any idea where you are?

(Cut to Mulder.)

MULDER: No, but I'm sure they'll find us. We probably lit up every spy satellite in this hemisphere. It was the only thing to do, Scully. If you're right about what's on this car, an explosion outside a populated area...

(Cut back to Scully.)

...would reduce the risks.

SCULLY: Mulder, if I'm right, they're not going to want to find you... but you don't think I'm right, do you?

(Cut back to Mulder.)

MULDER: We'll have to wait and see.

(Cut to Scully.)

SCULLY: We're not waiting for anything, Mulder, we got to get you...

(Cut back to Mulder.)

...out of there as fast as we can.

MULDER: I'm fielding all offers and suggestions.

(Cut to Scully, who drives rapidly, thinking. Cut back to the boxcar. The timer now reads 00:38:16.1. Mulder stares up at it.)

They're not going to come, are they?

(The Red-Haired Man is now sitting in the corner.)

RED-HAIRED MAN: I said you were making a mistake.

(Mulder starts towards him.)

MULDER: Tell me something. You got on this train to kill Doctor Zama, then what? What were your orders then?

(The Red-Haired Man looks around.)

Who are you protecting?

(Still, no answer is given.)

Unless that bomb is as phony as you are, we've both got about half an hour to live. Is that part of the plan?

RED-HAIRED MAN: They don't make provisions for saving my life.

MULDER: Well, what about that thing locked back there? What provisions were made for saving its life?

RED-HAIRED MAN: I don't know. I wasn't expected to fail.

MULDER: You know what it is, don't you? You're going to die for that thing. Is it important enough to die for? What is it, a plague carrier? A leper?

(The Red-Haired Man rolls his eyes a little and smirks, looking away. Mulder steps closer.)

We're both going to die in here. The difference is, I'm going to die quickly.

(He points his gun. The Red-Haired Man keeps smirking.)

As an employee of the National Security Agency, you should know that a gunshot wound to the stomach is probably the most painful and the slowest way to die... but I'm not a very good shot and when I miss, I tend to miss low.

(The smirk disappears from the Red-Haired Man's face as one appears on Mulder's.)

RED-HAIRED MAN: It's a weapon.

MULDER: A weapon?

(He lowers his gun and kneels down.)

What kind of a weapon?

RED-HAIRED MAN: Ask yourself, my friend. What could be more valuable than star wars? More valuable then the atomic bomb or the most advanced biological weapons?

MULDER: A standing army immune to the effects of those weapons. That's what Doctor Zama did, didn't he? He came up with an immunity to those weapons... and he was trying to smuggle that thing back to his own country to share the science, only our government isn't in the mood to share, right? They've been doing experiments since World War II, tests on innocent civilians... but Zama succeeded where the others had failed. And that thing in there...

(He stands.)

That's no innocent civilian. It's not a leper either. It's an alien-human hybrid, isn't it?

(The Red-Haired Man looks up.)

RED-HAIRED MAN: Then again, if that were true, you'd have expected someone would have been here by now to save it, wouldn't you?

(Mulder glares at him, then looks over towards the hybrid again.)

(Scully walks in and goes to the desk. She pulls open the drawers and shuffles through them. She finds a small black book and reads some of it. She then picks up the phone and dials a number.)

SCULLY: Yes, hello, my name is Dana Scully and I'm trying to reach Senator Matheson at home. I've already tried him at his office. Please, this is an emergency, can you reach him? Yes, I'm at, uh, 555-0199. Thanks. This area code.

(She hangs up. She then pulls out a roll of masking tape and rips off two pieces, taping an "X" to the window. Walking over to the TV, she puts in the autopsy video.)

(Mulder's phone rings. He walks over and picks it up. The Red-Haired Man is now in a chair.)

MULDER: Yeah.

SCULLY: Mulder? I think I've got something here.

MULDER: What is it?

(Cut to Mulder's apartment.)

SCULLY: I think I may have a code for you.

(She rewinds and plays at the same time. Zama puts on his medical garb and goes over to a keypad.)

I'm watching Zama punch it into a keypad in one of the train cars.

MULDER: What are you watching?

SCULLY: Your alien autopsy video.

(Cut to Mulder.)

MULDER: You mean I might get my twenty-nine ninety-five's worth after all?

(Cut back to Scully, who looks at her watch.)

SCULLY: I've got six minutes left, is that what you have?

(Cut to Mulder.)

MULDER: Let's hope not. What's the code?

(Cut to Scully, who watches on slow motion.)

SCULLY: One.

(Cut to Mulder, who walks over to the keypad. The Red-Haired Man watches him carefully.)

One, zero.

(Cut to Scully, who growls in frustration a little and rewinds just a bit, then presses play in slow motion again. Cut to Mulder.)

MULDER: Wait, are you there?

(He runs the keycard through the sensor. Cut to Scully.)

SCULLY: Yeah, yeah. One, zero, one.

(Cut to Mulder, who punches it in.)

MULDER: One, zero, one.

(Cut to Scully.)

SCULLY: And a three... then a three...

(Cut back to Mulder, who punches in the numbers.)

MULDER: Three, three.

(Cut back to Scully. Zama's hand obstructs the view of the last number. She rewinds and tries again.)

SCULLY: Uh... I can't see the last number clearly. His hand gets in the way.

(Cut to Mulder.)

MULDER: Tick-tick, Scully.

(Cut back to Scully.)

SCULLY: I know, I'm sorry, um... I think it's a one.

(Cut to Mulder.)

MULDER: You think it's a one? Are you sure?

(Cut to Scully.)

SCULLY: Yeah, yeah, I'm pretty sure.

(She nods, half-believing herself. Cut to Mulder.)

MULDER: One.

(He presses one. The keypad beeps and the lights turn green. He smiles then is struck from behind and collapses, dropping the phone. Cut to Scully.)

SCULLY: Mulder?

(She hears sounds of a struggle.)

Mulder?!

(Cut back to the train car. The Red-Haired Man effectively stomps a nature trail into Mulder, pounding him on the ground. He then straightens his suit and opens the door. He steps outside of the train car and is blown back in, having been shot. A man steps over him as he groans and moans in pain. X walks over to Mulder and rolls him over. Most of Mulder's face is covered with blood. X stares at him, then looks up at the bomb, which is down to a minute. X goes back to the alien and looks inside. He looks back at Mulder, then at the alien, trying to decide. Outside, he carries a body. Mulder's body. He walks just far enough to escape the ensuing explosion, carrying his ally to safety.)

(Scully walks down the stairs and into Mulder's office. He is on the phone. His face still bears the marks of the beating he took at the hands of the late Red-Haired Man.)

MULDER: No. Okay, call me if you learn anything.

(He hangs up.)

Nothing, Scully. Not the rail operators, not the forestry department. Nobody knows what happened to that train car.

(She takes off her coat and lays it across the back of a chair.)

SCULLY: Are there any satellite photos you can get your hands on?

MULDER: Senator Matheson hasn't returned my phone calls. His, uh... his aides say he's out of the country.

SCULLY: Well, the administrator at the hospital where you were admitted said that someone had called and alerted them to your location. Now, I went through the phone records myself, and the call was placed from a phone booth in Blue Earth, Iowa.

MULDER: Did you locate the briefcase that Zama left on the train.

SCULLY: Yeah. I got it right here.

(She pulls it out and hands it to Mulder. He walks over and sits down at his desk, opening it up.)

MULDER: This doesn't look like the same briefcase.

SCULLY: It's the one they gave me, the one they said you gave to the conductor.

(Mulder flips through the notepad. The writing is different.)

MULDER: These aren't the same journals. They've all been rewritten.

SCULLY: Mulder...

MULDER: They're getting away with it, Scully.

SCULLY: They've gotten away with it, Mulder. The bodies at the leper colony have all been removed.

MULDER: I know what I saw on that train car. It wasn't a leper and it wasn't human.

SCULLY: And I know what I saw at that research facility. It was barely recognizable as human.

(Mulder slumps back in his seat.)

Don't you see, Mulder? You're doing their work for them. You're chasing aliens that aren't there, helping them to create a story to cover the shameful truth... and what they can't cover, they apologize for. Apology has become policy.

(Mulder stands.)

MULDER: I, I don't need an apology for the lies. I, I don't care about the fictions they create to cover their crimes. I want them accountable for what did happen. I want an apology for the truth.

(They stare at each other.)

(An elderly Japanese man sits in a dark room, painstakingly translating the Japanese journals. A light flares from a match being lit. The Cigarette-Smoking Man raises the match to the cigarette in his mouth, lighting it. He takes a deep drag, proud of the success, then blows out the match.)

[THE END]