Season 9: Nothing Important Happened Today (1) (9X01)

Written by: Chris Carter & Frank Spotnitz
Directed by: Kim Manners

A man, Carl Wormus, intrigues a woman in a bar by mentioning that the government is adding chloramine to the water supply. They go for a drive together but as they near a drawbridge the woman grabs the steering wheel sending them plunging into the water. She grabs his ankle to stop him escaping.

Monica Reyes meets up with Assistant Director Follmer in his office. Follmer hands Reyes two videos which contain footage of the underground garage where Doggett and Skinner fought off "super soldier" FBI agents. But the video shows nothing out of the ordinary. Meanwhile, at a water reclamation facility, a worker is pulled underwater by the woman from the bar.

Doggett shows up at Scully's apartment to tell her that Mulder isn't living in his apartment anymore. Scully already knows but refuses to elaborate further. Skinner urges Doggett to drop his investigations. Scully agrees but Doggett tells her his supposed friend, Knowle Rohrer, had tried to kill him and Skinner in the garage.

Doggett gets home and finds a photograph of him and Rohrer in the marines so decides to find out about Rohrer. Coincidentally, the woman from the bar, Shannon McMahon, is also in the photo. McMahon sneaks into the FBI and leaves an envelope containing Wormus' obituary. Doggett pursues the lead by calling Scully into the morgue where she determines that Wormus drowned but notes the bruising on his ankle.

The Lone Gunmen tell Reyes that Doggett and Skinner left to investigate emails sent to Carl Wormus from a worker at the water plant named Roland McFarland - the man Shannon McMahon drowned. Doggett and Skinner sneak into the main control room where Doggett finds files relating to chloramine. Follmer tracks the men but Doggett slips into a filtration tank to get away. Suddenly Shannon McMahon surfaces and grabs hold of Doggett and pulls him under the water......

Notes:
The opening titles get a major revamp for this last season. The basic concept is still there, but some images are added. One shot shows a list of "FBI Contacts, Witnesses, and Contributors." The names on this list are actually the screen names of posters on the official "X-Files" message board and changed with each new episode that season. Other names on the list were anagrams of characters on the show.

The character of Brad Follmer is named after creator Chris Carter's writing assistant.

When Doggett meets with the Lone Gunmen, their faces are blue. This is a reference to an incident in the series finale of "The Lone Gunmen", "All About Yves".

"Nothing important happened today" (or words to that effect) was the entry King George III of England made in his personal diary on 4 July 1776. (Since he could not have known about the events occurring in the colonies for several weeks, his comment is often cited as a bit of historical irony.)

Quotes:
Assistant Director Follmer: Monica?
Reyes: Hi.
Assistant Director Follmer: What are you doing?
Reyes: I was leaving you a note. Your assistant was out and I didn't want to knock. I was going to call you... Hi, Brad.
Assistant Director Follmer: Come on in. (As Reyes enters the office, Assistant Director Follmer kisses her) What?
Reyes: We're at work.
Assistant Director Follmer: You used to ask me to close the door at work back in New York.
Reyes: Is that all you called me here for, Assistant Director?
Assistant Director Follmer: I probably shouldn't tell you how hot you look either, because you do. How long's it been? Two years?
Reyes: Yeah. We should catch up, Brad. Really. I've got to get downstairs.
Assistant Director Follmer: I've got something for you. (He takes a pair of video tapes out of his desk drawer) Forgive me, but... it didn't take a whole lot of digging to figure out why you're here in DC, Monica.
Reyes: What are those?
Assistant Director Follmer: Something you're going to see, but... I wanted to show you first. They were taken from the security cameras in the FBI parking garage. One of them... shows you arriving in a cab meeting John Doggett.
Reyes: Yeah, I'm working with him. He called me up here on a case.
Assistant Director Follmer: I heard. Believe me, this whole thing about a... chase and a crash and a fire. And now Doggett's internal investigation of Deputy Director Kersh, it's... big news"
Reyes: What's so important to show me? What's on the other tape?

Skinner: I don't know where Mulder is. I don't know that I'd tell you if I did.

Reyes: (to Doggett) I checked with movers, airlines, car rental agencies... No Mulder.
Doggett: Somebody get to him, that it? Doesn't seem possible, does it? (to Skinner) Okay, so where's that leave us? It's just me and you, our word against Kersh and the FBI.
Reyes: You'd better sit down, John. It's more complicated than that.
Doggett: What's more complicated?
Reyes: This investigation.
Doggett: What about it?
Skinner: I want to ask you to drop it.
Doggett: No, not from you. Not from you. Not after what we've been through. I mean, we barely escaped with our lives.
Skinner: That's something worth thinking about.
Doggett: I'm sorry, you're not that reasonable. What, did they get to you, too?
Skinner: No one got to me, John, they didn't have to. That's the point.
Doggett: You're afraid of them.
Skinner: I'm not afraid of them.
Doggett: Well, you're afraid of something. What? The real tape showing up? Them calling you a killer for you having to shoot Alex Krycek?
Skinner: No, I'll stand by my actions, Agent Doggett, but I won't stand by yours if you're going to continue to push and push until you get somebody killed. You want to know what I fear? I fear for Mulder and Scully. I fear for the life of that child if you don't stop pushing, John.
Doggett: You don't think I fear for those things, same as you?
Skinner: If you did, you'd let it go.
Doggett: So what I'm hearing is... if I don't drop it, I'm alone on this.
Reyes: John. You're not.

Doggett: I'm really sorry. I... Dana, I need your help.

Scully: I don't know how to find him.
Doggett: It just doesn't make any sense. Mulder leaving you here all alone. Just walking out on you, not telling you where and why.
Scully: It makes sense in its own way. That's all I can tell you.
Doggett: Then tell me why you can't trust me. Everything I did to try to protect you when you thought your baby was in danger. What changed? Why is it suddenly I'm now the enemy?
Scully: Let it go, John. Drop it. Please.
Doggett: These people tried to kill me. They tried to kill AD Skinner. They would have killed Mulder, too. They're still out there, Dana.
Scully: Exactly right, and they are unstoppable, and they are inside the FBI.
Doggett: You know something you're not telling me. Mulder knows something. How long can you hide from it? Knowle Rohrer, this old military buddy of mine, he told me your pregnancy was a result of a Government cloning experiment to try to create what he called a Super Soldier.
Scully: I don't want to hear this. Look, there is nothing to any of this.
Doggett: Knowle Rohrer, my buddy, was one of the men that tried to kill us in the FBI garage.
Scully: My baby... my son... is fine.
Doggett: I hope to god that's true. I just don't want to pretend.
Scully: I'm going to ask you to leave. I'm going to ask you to leave and not come back here.

Scully: Water. Asphyxiation induced by the inhalation of water. There's contusions on the forehead and on the chest but the impact isn't what killed him. This man drowned. You're looking at me like you hope that there's something more, but there isn't.

Reyes: I'm sorry, that's not it. I'm just impressed that you can do this.
Scully: This is what I do, Agent Reyes.
Reyes: But you're here doing it now. Something did happen, didn't it. I know what you're afraid of. That there's something wrong with your baby.
Scully: We can let our fears get the better of us. We can... imagine things, make connections with things that aren't there. Like with this man.
Reyes: If you ever feel the need to talk to someone, Dana, I'm here. I'd never betray a confidence.
Scully: There is something.
Reyes: What?
Scully: Right here on the ankle.
Reyes: Are those... fingerprints?
Scully: Yeah, that's what they look like.
Reyes: From someone holding him down?
Scully: I don't know how, or who.

Episode Number: 183
Season Number: 9
First Aired: Sunday, November 11, 2001
Production Code: 9A01

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Season 8: Existence (8X21)

Written by: Chris Carter
Directed by: Kim Manners

A pathologist is called in late at night to examine the gnarled body of Billy Miles (crushed in the garbage truck in 8X20). The doctor pulls from the remains a piece of metallic vertebrae and, thinking it is most likely trash, places it on a nearby lab tray. He leaves the office with plans to continue the autopsy in the morning. The metal magically spins on the tray and reproduces itself, progressively growing larger.

At the FBI, Mulder produces a video grab of a healthy and re-formed Billy Miles walking out of the morgue the previous night. Krycek explains to Skinner and Doggett that Billy is a human replacement -- a new kind of alien created to repopulate the planet. Although Billy may not find the hiding Scully, Krycek warns that others like him will.

Agent Crane interrupts to tell Doggett that Knowle Rohrer is in the building to see him. Rohrer fabricates a story to Doggett that his investigation is military in nature and stemmed from a plan to create a super soldier. He explains that Billy is a prototype who is now after Scully because she was abducted by the military and impregnated with such a prototype.

The chip in her neck was used to monitor her. When Rohrer asks where Scully is, Doggett claims ignorance. Meanwhile, Billy Miles enters the FBI hallway, unnoticed by everyone but Krycek. When Krycek bolts out of Skinner's office, Skinner follows him into an elevator to flee Billy. As the doors shut out Billy, his hand penetrates the metal and goes straight into the elevator chamber. Billy swings his arm and cuts into the top of Skinner's head, which knocks out the A.D. While Skinner later recuperates in the hospital with a concussion, Doggett tells Mulder that his informant Rohrer tipped him off that this would happen. Doggett is concerned that his knowledge of Scully's whereabouts may eventually catch up with him.

Scully and Reyes drive through the night into Democrat Hot Springs, Georgia. Although it was once the city where Doggett was born, it is now a deserted ghost town. They set up camp in an abandoned house of worship that has no running water. That evening, Reyes goes outside to have a nerve-settling cigarette, when a light in the sky catches her eye. While too low and bright to be a star, it is unidentifiable. She ignores it and goes back inside.

Seeing the newly cleaned building, Scully thanks Reyes for her kindness and tells the agent that she reminds her of her late sister, Melissa. Reyes sees someone lurking outside and draws her gun. A truck driven by a female game warden comes barreling toward her. The agents explain that Scully's life is in danger and that they are in hiding. The warden kindly gives them her first aid kit and a camp stove before leaving. Reyes admits to Scully that her vibrations are inclining that something feels off about the abandoned place.

When she goes outside to get more water, she again sees the light in the distant sky. While she is watching it, Billy Miles appears and throws her against a wall. Before he can attack her, a gunshot blows a hole through his chest. The game warden stands aside, her rifle still smoking. Reyes sees the alien vertebrae on Billy's neck, and she and the warden carry his limp body to show Scully that he's dead. Scully, still worried that he can never be killed, announces that she is going into labor.

Sitting in the FBI garage, Doggett asks Mulder when his quest is going to end. Mulder responds that perhaps it never will. They see Krycek pulling into the garage. His passenger is the ubiquitous Knowle Rohrer. Doggett follows Rohrer into the FBI building, finding him surreptitiously meeting with Agent Crane. Hiding from them, he meets up with Skinner, and they call Mulder with news about Crane. Mulder, still in the garage watching Krycek, says that Krycek, Rohrer and Crane are all in it together, fooling the agents into believing that they are protecting Scully.

Mulder tells Doggett to get out of there and asks him to reveal where Reyes took Scully. Suddenly, the car window smashes and Krycek holds Mulder at gunpoint. Krycek says that he tried to stop the aliens but it is now too late. Although he has protected Mulder's life in the past, Krycek explains that he is forced to kill him now because the conspiracy goes deep into the FBI. Krycek cocks his gun trigger and aims at Mulder, but Skinner shoots him in the arm. Krycek pleads with the A.D. to kill Mulder, insisting that he can save more lives that way. Skinner listens, but then shoots Krycek squarely between the eyes, killing him.

Mulder takes off to the airport in pursuit of Scully. Upstairs in the building, Doggett pulls his gun on Rohrer and Crane, and they chase him. Doggett runs into Skinner, and the two break for their car. They run over Crane, but he is still alive, hanging onto the side of the vehicle. Crane smashes through the window, while Rohrer follows in another car. Skinner sideswipes a concrete pole, ridding him of Crane. When Crane gets up, Rohrer's car hits him and swerves out of control. Rohrer crashes into a wall, and his car explodes.

Reyes is preparing for Scully's birth when she notices the alien vertebrae on the game warden's neck. She throws boiling water on the warden, screaming Who are you? Suddenly, a number of cars pull up to the abandoned town and a perfectly healthy Billy Miles gets up off the ground. This baby will be born, the replicant game warden says. Scully screams in pain, watching as a crowd of aliens walk into the building and surround her.

This is my baby! Please don't let them take it, she pleads to Reyes. The aliens watch silently as Scully gives birth with Reyes' assistance. Mulder flies overhead in a helicopter and the aliens pull away in their cars. He lands, and runs toward the building, calling out for Scully. Reyes orders him to take Scully to the hospital.

The Gunmen depart, and Scully shows Mulder the baby, whom she named William, after Mulder's father. Although the baby is completely human, they comment that he is still a miracle. Mulder believes that the aliens did not take him because they thought he would be otherwise. I think we feared the possibility, he tells Scully. The truth we both know. And as he cradles their son, he leans in and kisses her.

Notes:
This episode marks the time that Mulder and Scully finally become a couple.

This episode marks the death of recurring villain Alex Krycek, although he appears in a hallucination during the finale.

This episode was not supposed to end with a passionate or more-than-friendly kiss between Fox Mulder and Dana Scully, however David Duchovny and the episode's director, Kim Manners, told Chris Carter that they felt this kiss was absolutely necessary, so the episode uses that. It subsequently is used to (more or less) justify that Mulder is in fact the father of William.

After taping the last scene of the episode, the one in Scully's apartment, David and Gillian stayed on the set crying for 5 minutes. It was their way of saying goodbye to the relationship that they built, as characters and actors.

Quotes:
Mulder: This is a video grab from a DC morgue. It's Billy Miles.
Skinner: How can that be?
Doggett: It can't be. It's impossible.
Mulder: Yeah. It can't be, but it is. Walking out of the morgue looking like a new man.
Doggett: His body was taken to the morgue in a little box, for god's sake.
Krycek: Like I told you. You can't stop him.
Skinner: Yeah, you know, you keep saying that, Krycek. So why don't you explain it to us, because I'm having a little bit of a hard time understanding it myself. Billy Miles was scraped out of the back of a garbage truck. I saw him go in, I saw him come out.
Krycek: Well, I don't know if I can explain it in any technical sense, but... that's Billy Miles, without a doubt.
Skinner: You're sitting there for one reason, Krycek. Because you can explain it.
Krycek: I told you — he's a human replacement. Some new kind of alien... created to aid in the repopulation of the planet.
Mulder: Which Scully is a threat to.
Krycek: If she has that baby.
Doggett: Well, I don't care who he is, or what you think he's made of, there's no way he's going to find her. No way.
Krycek: Well maybe he's not, but there are others out there just like him. And it's only a matter of time before they will.

Doggett: It's not like you, Knowle coming to see me when you make me work so hard to see you.

Knowle Rohrer: This couldn't wait, John. It's about this thing you're pursuing.
Doggett: This thing?
Knowle Rohrer: This man you're after. I think you know what I'm talking about.
Doggett: I think I'm confused, Knowle — if it's a man or if it's a thing.
Knowle Rohrer: It's military, John. It goes all the way to the top. I can't overstate the sensitivity. Let me say there was a rumoured program out of the cold war. A plan to create a super soldier.
Doggett: Well, this kid I'm talking about was pretty damn super. Got right up out of a gut bucket and hit the ground running. Kid wasn't exactly what I'd call military material. In fact, they say he was an alien abductee.
Knowle Rohrer: You got it half right, John.
Doggett: Which half?
Knowle Rohrer: What you're chasing... is a prototype.
Doggett: Uh huh. And this so called prototype... what is he after?
Knowle Rohrer: Oh, I think you know that, too, John. He's after your partner, Scully. You may not be aware that she was part of a program herself. Six years ago, Agent Scully was taken in a military operation staged as an abduction. They put a chip in the back of her neck to monitor her. It was also used to make her pregnant with the first organic version of that same super soldier.
Doggett: Huh. What do you want from me?
Knowle Rohrer: Help us catch him so we can put him down... before he finds her.
Doggett: You assume I know where she is.
Knowle Rohrer: Who does? Your superior? Whoever knows, his life's in danger, too. I want you to know.

Mulder: Hey. You know, how is it that this friend of yours is so desperate for your help? And then when we want to reach him, all of a sudden he's unreachable, nowhere to be found?

Doggett: I don't know, maybe he got wind. Maybe he got spooked. But I'm beginning to think it doesn't make a damn bit of difference.
Mulder: You told me that he told you he knew how to stop Billy Miles. Are you telling me now that you think he's a liar?
Doggett: He is or he isn't. What the hell difference does it really make?
Mulder: It doesn't make any difference at all. Unless you want to protect Scully and that baby.
Doggett: And then what? How long can you keep this up? How long until the next Billy Miles rears his head? The next threat? The next phantom? You ever stop to ask yourself? All the sacrifice, the blood spilled — you've given nearly a decade of your life. Where the hell is it all going to end?
Mulder: I don't know. Maybe it doesn't. Start the car.
Doggett: What?
Mulder: Alex Krycek just pulled in.
(Doggett starts the engine and follows Krycek's car through the garage. Krycek parks and Doggett stops nearby)
Doggett: What the hell is he doing here? How did he get security clearance?
Mulder: You recognise his passenger?
Doggett: Yeah. It's Knowle Rohrer.

Krycek: Get out of the car. Doesn't seem fair now. Doesn't seem right. Coming down to this.

Mulder: What do you know about fair or right, Krycek? You're a coward.
Krycek: I could've killed you so many times, Mulder. You've got to know that. I'm the one that kept you alive. Praying you'd win somehow.
Mulder: Then there really is no god.
Krycek: You think I'm bad. That I'm a killer. We wanted the same thing, brother. That's what you don't understand.
Mulder: I wanted to stop them. All you wanted was to save your own ass.
Krycek: No. I tried to stop them. Tried to kill... Scully's baby to stop them. It's too late. The tragedy's that you — you wouldn't let it go. That's why I have to do this. 'Cause you know how deep it goes. Right into the FBI.
Mulder: You want to kill me, Alex, kill me. Like you killed my father. Just don't insult me trying to make me understand.
(Krycek's finger slowly tightens on the trigger. A gun is fired, Krycek gasps in pain and falls. There is a bullet wound in his right arm. He looks up and sees Skinner, gun in hand. Krycek reaches down to pick up his dropped gun, screams in pain and falls to the ground again as Skinner shoots him in the arm again)
Krycek: It's going to take more bullets than you can... ever fire to win this game. But one bullet... and I can give you a thousand lives. Shoot Mulder.
(Skinner fires again and Krycek falls to the ground, a bullet hole between his eyes)
Mulder: I'm going to go to the airport. I need that location from Agent Doggett. Skinner, are you with me?
Skinner: You just go. I'll get him.

Deputy Director Kersh: I'm to take this story seriously? These incidents at the FBI. This account of Agent Scully's birth. I'm to submit this report as quality investigative work? As representative of actual fact?

Doggett: I signed the report there, sir.
Deputy Director Kersh: Yeah, I see it, John. And I see her signature here, too. On an X-File. I'd like to know when you assigned yourself, Agent Reyes.
Agent Reyes: Agent Doggett assigned me, sir.
Deputy Director Kersh: Agent Doggett cannot just assume the authority of this office.
Doggett: I assume it, because this office is under investigation. For the late night meeting between you, Agent Crane, and an intelligence operative named Knowle Rohrer.
Agent Reyes: Both men were presumed dead, but are now missing. In actual fact.
Deputy Director Kersh: You investigate what I tell you.
Doggett: And you put me on the X-Files. That's what I'm investigating.

Mulder: How's everybody doing?

Scully: We're doing just fine. (She gets up and carries the baby to Mulder)
Mulder: Hey, now. What are you going to call him?
Scully: William. After your father.
Mulder: Well, I don't know. He's... he's got your colouring and your eyes. But he looks suspiciously like Assistant Director Skinner.
Scully: I don't understand, Mulder — they came to take him from us — why they didn't.
Mulder: I don't quite understand that either. Except that maybe he isn't what they thought he was. That doesn't make him any less of a miracle though, does it?
Scully: From the moment I became pregnant, I feared the truth... about how... and why. And I know that you feared it, too.
Mulder: I think what we feared were the possibilities. The truth we both know.
Scully: Which is what?
(Still holding the baby between them, Mulder leans down and kisses Scully)

Episode Number: 182
Season Number: 8
First Aired: Sunday, May 20, 2001
Production Code: 8X21

Season 8: Essence (8X20)

Written by: Chris Carter
Directed by: Kim Manners

Mrs. Scully sets up decorations in Scully's apartment in preparation for a baby shower. She pesters her secretive daughter about whether the baby is a boy or a girl. Yet Mrs. Scully has a surprise of her own - she has hired Lizzy Gill, a baby nurse, to tend to the reluctant Scully. During the party, Lizzy goes into the bathroom undetected. She opens one of Scully's prescription bottles and dumps its contents down the toilet. Then she removes a packet of pills from her pocket and pours them into the bottle.

Dr. Lev (last seen in 8X08 ''Per Manum'') is working late at night in the Zeus Genetics lab, clutching an alien baby when Billy Miles (last seen in 8X15 ''Deadalive'') enters. Your work here is done, Billy says. He beheads the doctor with his hand and sets fire to the body. The next day, Doggett is home when Mulder pays him a surprise visit. He shows Doggett a news report on television of a fire at Zeus Genetics. Mulder believes that somebody is covering up whatever was going on in that lab, and Doggett sends Agent Crane to sift through the ashes at the crime scene. The only person not accounted for is Dr. Lev, a partner in Zeus with Dr. Parenti, Scully's former obstetrician. Mulder and Doggett break into Parenti's office and are surprised to see the doctor there. When Doggett finds racks of specimen jars with abnormal fetuses, Mulder accuses the doctor of experimenting with alien embryos.

Lizzy Gill leaves Scully's apartment and is picked up by Duffy Haskell. I think she trusts me, Lizzy tells him. In his office, Dr. Parenti packs up the specimen jars when he hears someone come in. It is Billy Miles. Parenti tells him that the office is closed. Mulder and Doggett sneak into Parenti's office in the middle of the night, suspecting foul play when the doctor does not answer their calls. Amid the fetuses, Doggett finds the head of Dr. Parenti in a specimen jar.

Suddenly, Billy Miles surprises Mulder and throws him through a glass window. Doggett, seeing the alien vertebrae on Billy, shoots at him but Billy escapes. Later, Scully tends to Mulder's injured head at her apartment. He tries to explain that Billy has transformed into an alien, but that he himself was somehow prevented from this through Scully's procedure in the hospital. Yet Billy is no ordinary alien, because Doggett saw red blood when he shot at him. Mulder determines that Billy is now a hybrid, and fears for the safety of Scully's baby. Lizzy, overhearing their conversation, phones Duffy. Duffy, however, is face-to-face with Billy Miles, and the alien slices off Duffy's head with one clean chop of his hand.

Duffy's body is found in an illegal medical facility used for cloning. There, Skinner locates prenatal records on Scully, as monitored by Dr. Lev and Dr. Parenti. Skinner takes Mulder aside and asks about the nature of Scully's conception, but Mulder, surprisingly, doesn't have any answers. Mulder calls Scully and says it is important that he immediately see her regarding interference with her pregnancy. Yet she hears a noise in her apartment and catches Lizzy tampering with her prescription bottle. Who are you? she demands. Later, after a checkup, the doctor assures Scully that the pills she had been taking were only harmless vitamin supplements.

Doggett interrogates Lizzy, who recounts how she worked as a research scientist on human cloning. Her research team had been successful at birthing an alien egg in a human mother. Mulder is outraged. What did you do to Scully? he screams. Lizzy tells them that there is nothing wrong with Scully's child. In fact, it is perfectly human, and she had tried to protect it. Agent Crane informs Doggett that Billy Miles phoned in and offered to give himself up.

A SWAT team storms Dr. Parenti's office, but Billy is not there. Sensing danger, Mulder orders Scully to quickly pack and leave her apartment. Doggett calls with news of Billy's disappearance, and mysteriously, the lights go off in Scully's apartment. Billy misses Mulder and Scully as they escape outside. Their car, however, is blocked in, and the approaching Billy Miles traps them like sitting ducks.

Suddenly, another car screeches from out of nowhere and plows over Billy. Mulder and Scully watch in shock as its driver - Krycek - orders them to get in. Billy Miles gets up, unhurt, and watches the car speed off. At the FBI, Krycek informs the assembled agents that the aliens are afraid of Scully's child because it is greater than they are. Doggett is suspicious of Krycek and calls Agent Monica Reyes, who has flown into Washington, for help.

Skinner and Mulder take Scully into the elevator, but as they approach the garage, Doggett calls to say that Billy Miles is down there. They put Scully back in the elevator, and Billy goes up the stairs. Krycek takes Scully while Skinner and Mulder proceed in the elevator, with Billy in pursuit. Doggett puts Scully in a car with Reyes. On the roof, Billy is about to strike Skinner when Mulder comes up from behind to push Billy off the roof. He lands in a garbage truck and its compactor crushes him. As Scully and Reyes speed out of the garage, Agent Crane blocks their path. He watches as the garbage truck rids of Billy, and then waves the women safely by. They do not see that Agent Crane too has the alien vertebrae on his neck.

Quotes:
Mulder: (voiceover) We call it the miracle of life. Conception: A union of perfect opposites — essence transforming into existence — an act without which mankind would not exist and humanity cease to exist. Or is this just nostalgia now? An act of biology commandeered by modern science and technology? God-like, we extract, implant, inseminate... and we clone. But has our ingenuity rendered the miracle into a simple trick? In the artifice of replicating life can we become the creator? Then what of the soul? Can it, too, be replicated? Does it live in this matter we call DNA? Or is its placement the opposite of artifice, capable only by god. How did this child come to be? What set its heart beating? Is it the product of a union? Or the work of a divine hand? An answered prayer? A true miracle? Or is it a wonder of technology — the intervention of other hands? What do I tell this child about to be born? What do I tell Scully? And what do I tell myself?

Margaret Scully: You know, it would be a whole lot easier for everyone if you would just tell us the sex, Dana. Did you hear me?

Scully: Yes, I heard you, Mom — for about the thousandth time, you can wait. Didn't you have to wait with us?
Margaret Scully: Well, I know it's a boy. I can just tell by the way you're carrying. It's a boy.
Scully: Well, see, you obviously don't need me to tell you because you already know.
Margaret Scully: Then it's a boy? Oh, it's the least you could tell your mother considering everything else you're keeping a secret. (There is a knock at the door)
Scully: We told people noon, right?
Margaret Scully: Mm-hmm.
(Scully opens the door. Lizzy Gill enters, carrying two bouquets of flowers, one pink one blue)
Lizzy Gill: Hi. Your mom said to cover all the bases. I'm Lizzy Gill.
Margaret Scully: Hi, Lizzy. Let me give you a hand with that. I asked Lizzy to help out today.
Scully: Oh. Hi.
Lizzy Gill: These are going to need some water. Congratulations, by the way.
Scully: Mom... what do we need help with?
Margaret Scully: I don't know. It's just, well you shouldn't have to worry. You have to let people do for you. She's a very highly recommended baby nurse, by the way.
Scully: Oh, Mom.

Mulder: Knock, knock.

Doggett: Right. We get caught in here, what are you going to say then?
Mulder: I'll just say I'm with you, Agent Doggett. It's Saturday anyway, right? We're just having a look around.
(Doggett enters a room lined with jars of foetuses)
Doggett: Hey, Mulder.
(Mulder goes to join Doggett, but is intercepted by Dr Parenti)
Dr Parenti: Who are you?
Mulder: Me?
Dr Parenti: Yes, you, sir. What do you think you're doing in this office?
Mulder: I'm with an FBI agent who would like to ask you the exact same question. Dr Parenti, isn't it?
Dr Parenti: I'm in the middle of a very delicate medical procedure. Whatever you want, you don't just come barging in here. I don't care who you are.
Doggett: This medical procedure... it have anything to do with this?
Dr Parenti: Please...
Doggett: Why don't you tell us what we're looking at here, Dr Parenti?
Dr Parenti: You people have no right to be here. I want you to leave.
Mulder: What is this? Some kind of showroom?
Dr Parenti: Do you know what I've been through in the past 24 hours? Close friend and colleague is missing. Much of my life's work has been destroyed.
Doggett: How about you explain what you are doing? What these things are.
Dr Parenti: They are what we are all working so hard to prevent — children with non-survivable birth defects.
Mulder: Does that work include experimentation with alien embryos? Work that you would destroy to cover up such allegations?
Dr Parenti: Where do you get these ideas?
Mulder: From a friend of mine — a former patient of yours — Dana Scully.
Dr Parenti: If I'm such a Dr Frankenstein how is it that Ms Scully is carrying a perfectly healthy child? In her own medical opinion.
Mulder: Is she?
Doggett: I'd say this man's suitably pissed off. Why don't we let him get back to work. Let's go, Mulder.

Mulder: Ahh! Scully.

Scully: Sorry.
Mulder: I see why you gave up a career in medicine for the FBI, Scully. You've got manos de piedra.
Scully: Sorry.
Mulder: Imagine if he'd really connected.
Scully: Who?
Mulder: Billy Miles.
Scully: Billy Miles? He did this?
Mulder: Ask Agent Doggett. He saw him.
Doggett: If you ask me, the kid was whacked out on something. Whatever it was, he's feeling no pain.
Mulder: Ask me, the kid isn't a kid.
Doggett: Oh, don't tell me he's an alien.
Mulder: He is a type of alien. A human replacement. One who looks human. Look at his strength. The way he took those slugs.
Doggett: I've seen plenty of guys whacked out on chemicals, keep on coming.
Mulder: Well, then, you're ignoring who Billy Miles is. You, of all people, Agent Doggett who's supposedly running the X-Files.
Doggett: You're ignoring the fact that he bled red blood. Now, every single X-File I read — and I read them all, Mulder — what you call 'aliens' bleed green, right?
Mulder: Well, Billy Miles is a whole new deal. He's an alien abductee who was returned after hideous procedures were performed on him. And who miraculously returns to so-called perfect health when his body completely sheds its skin.
Doggett: Same thing happened to you.
Mulder: Same thing would have happened to me if I'd been left alone. If Scully hadn't treated me.
Scully: What I want to know is what Billy Miles was doing at that medical office.
Mulder: Same as when he torched Zeus Genetics and destroyed their experiments with alien biology and the doctors performing them.
Scully: And what were you doing there... Mulder?
Mulder: Looking for answers.
Scully: To what?
Mulder: One of those doctors was your doctor.
Scully: Mulder...
Mulder: Listen, Scully, I'm sorry, but I just need to know that this baby of yours is going to be all right.
Scully: My baby is fine, Mulder. I've had it checked over and over again with my new doctor that I trust implicitly.

Lizzy Gill: I knew people would kill for what I know but... not like this.

Doggett: Not going to let that happen. Just what you told me and Agent Crane.
Lizzy Gill: For the past ten years I've been working as a research scientist trying to produce human clones — long before the media circus with sheep and cows. The work was painstaking, largely unsuccessful, but there was a lot of interest and a lot of money.
Mulder: Money from who?
Lizzy Gill: Orders came from government men. But they're all dead now.
Mulder: But the work continued.
Lizzy Gill: We were surprisingly successful with a clone from a human egg and alien DNA. DNA that the government had since 1947.
Skinner: What do you mean by success?
Lizzy Gill: Alien babies. Birthed by human mothers desperate to conceive. They didn't live more than a couple of days, but tissue and stem cells is what we were after for other experiments.
Mulder: What other experiments?
Lizzy Gill: I don't know anything about that. But I know it was something good.
Mulder: What did you do to Scully?
Lizzy Gill: We were trying to protect her.
Mulder: What did you do to her?
Lizzy Gill: No, you don't understand.
Mulder: Tell me what's wrong with her! Tell me what's wrong with her baby!
Doggett: Listen to her. What she's saying.
Lizzy Gill: There's nothing wrong with her. That's what I'm trying to tell you. The child she is carrying is very special. One could only hope to create that in a lab. A perfect human child, but with no human frailties.

Krycek: You should all know exactly what it is you're up against... what Agent Scully's up against.

Doggett: You realise you're all listening to someone who tried to kill me. He left you for dead.
Mulder: Tell us about Billy Miles.
Krycek: There are others just like him. You can call them what you want. They're human replacements, alien replicants. They're virtually unstoppable.
Skinner: What do they want?
Krycek: They want to knock out any and all attempts by us to survive the final days — when they come back to retake the planet.
Doggett: So, what, they're wandering around among us... looking for trouble? Some kind of alien lawmen?
Krycek: You saw what they did to those doctors. They're fearless. And they answer to no one, except their own biological imperative... to survive.
Mulder: What about Scully? What do they want with her?
Scully: They want my baby. Why?
Krycek: They didn't even know about it. I don't know exactly how they could have found out just how... how important it is... how special.
Scully: My baby is normal.
Krycek: Your baby was a miracle. Born of a barren mother's barren womb.
Mulder: Are you saying that they're afraid of it?
Krycek: They're afraid of its implications. That it could somehow be greater than them. Something... more human than human.
Scully: I don't believe this.
Skinner: You wanted to destroy her child.
Krycek: I wanted to destroy the truth before they learn the truth.
Mulder: That there's a god... a higher power.
Doggett: I don't believe this crap; I don't believe you're all sitting around here listening to it even when you know this man's a liar. Worse than that.
Krycek: You can believe what you want, but I don't think you can take the chance that I'm wrong. There isn't hospital that's safe enough. She may never even make it out of this building.
Doggett: Why don't you just shut up?
Mulder: Agent Doggett. Get on the phone. If we're going to get Scully out of here we're going to need some help.

Episode Number: 181
Season Number: 8
First Aired: Sunday, May 13, 2001
Production Code: 8X20

Season 8: Alone (8X19)

Written by: Frank Spotnitz
Directed by: Frank Spotnitz

In a small house in Ellicot, NY, Gary Sacks tends to his ailing father, Arlen. Gary goes into the kitchen, and Arlen panics when he sees something on the ceiling. Gary hears the heart monitor flatline in the other room and sees that his father has disappeared from his wheelchair. Gary looks for him and hears a hissing sound. Suddenly, a huge reptilian face lunges at him, and he is sprayed with venom.

At the FBI, Scully cleans out her desk in preparation for maternity leave. She finds memorabilia from past cases, and gives Doggett an Apollo 11 key chain that was given to her by Mulder (in 4X17 Tempus Fugit). The medallion symbolizes teamwork and partnership, and she thanks Doggett for his help over the past year. She exits the office. Moments later, Agent Leyla Harrison enters, having been assigned to partner with Doggett on the X-files during Scully's leave. Harrison, a fan of Mulder and Scully's work, is excited about being on an actual X-file and accompanies Doggett in examining the crime scene at the Sacks' home. There are some remnants of slime in the home and near where Arlen's body was found. Based on her study of Mulder and Scully's past cases, Harrison immediately jumps to otherworldly conclusions about the nature of the slime. Doggett shoots down her theories.

Doggett wanders alone toward a deserted mansion near the crime scene, and after entering, finds a book on the Sixth Extinction on a desk. He hears a noise and pulls out his gun, only to find Agent Harrison. He tells her that it is here and orders her to wait outside. Gunshots ring outside, and he looks for Agent Harrison, but she has disappeared. He goes into the nearby woods and accidentally falls through a trap door on the ground. He finds himself in some sort of underground wine cellar.

Mulder assists Scully in going to her Lamaze class. She admits to feeling like she has deserted her work. Mulder assures her that Doggett can take care of himself. Skinner, meanwhile, leads a pack of agents to search for Doggett. Scully is worried, and expresses a desire to go back to work to help the search. She performs an autopsy on Arlen Sacks' body and discovers that the slime on his body is actually venom that has been excreted by a reptile. Mulder tries to convince her to stop working as he steps in to conduct his own investigation.

In the underground lair, Doggett is wondering what to make of an amber-colored shell of a dog when he sees something quickly move past him. A giant, snake-like creature attacks him and sprays venom in his eyes. With his sight impaired, Doggett shoots blindly at the creature, and it manages to get away. Harrison hears his gunshots and finds Doggett. Her eyes are also affected, but she brings him to the sickly body of Gary Sacks.

Mulder arrives at the crime scene where Skinner is redirecting the search farther away. Mulder, no longer an FBI agent, takes off into the woods on his own and comes upon the mansion. He sees something in the brush and picks it up, but is startled by Herman Stites who claims to own the property. Mulder asks him if he has seen a reptile and the man bristles at any accusations. Mulder walks away and misses Doggett, who has climbed up to a grating and is calling out to Stites from below. I need a hand, he begs Stites, who ignores the plea. Stites steps on Doggett's outstretched hand, and the agent falls back down in the cellar. Doggett and Harrison hear Stites seal the trap door closed. They then realize that Gary Sacks' body is gone.

Scully calls Mulder to tell him that Skinner is angry that he is tampering with a federal investigation. Mulder believes that it may be a man and not a reptile that they are looking for. He found the Apollo medallion and believes that Doggett is probably still nearby and that Stites is somehow involved. Doggett and Harrison blindly walk through the tunnel in the cellar. She fears that she is afflicted with the same thing as Sacks, because she has become completely blind. The creature appears once again and Doggett wildly shoots at it, but it gets away. Harrison finds Sacks' body. It has deteriorated even more.

Mulder sits in his car near the mansion, waiting. Scully discovers that the venom hardens the body's skin to form a shell. Then, its organs liquefy. She tells Mulder that Stites had been working on creating a new species of reptile. Mulder takes off after something moving in the woods. He watches as a human-sized reptile climbs up the house and into the window of the mansion. As Mulder bangs on the front door, he does not see the creature morph into Stites. Mulder confronts Stites, and Stites brings him into the underground wine cellar. There, Mulder sees Doggett and Harrison, who senses that Stites is really the creature. Suddenly, Stites disappears and the creature crawls along the ceiling. Without an issued gun, Mulder orders a blinded Doggett to shoot at the monster, but Doggett can't see what he's shooting at. Mulder demands that Doggett aim for the sound of his own voice. Although Doggett is hesitant about firing towards Mulder, he shoots and hits the creature. It transforms into Herman Stites, who lies there dead.

At the hospital, a healed Doggett checks in on Harrison. She will not return to the X-files. Mulder hands Doggett the Apollo medallion, but he asks that they give it to Agent Harrison. Mulder and Scully visit with Harrison, who asks them about a past investigation. As they reminisce with the agent, Doggett walks away down the long hallway, heading back to work - alone.

Notes:
Agent Leyla Harrison was named for X-Files fan Leyla Harrison, whose life was tragically cut short in February 2001 when she lost her battle with skin cancer.

Much like a real fan of the show, Leyla is full of information about the X-Files and makes references to several cases including ''Squeeze''/''Tooms'' (the liver eating mutant), ''The Beginning'' (an alien who sheds its skin), and ''Detour'' (the subterranean men). In the end she asks Mulder about how he saved Scully from the spaceship, referring to the feature movie ''Fight the Future''.

When Scully is cleaning out her desk, the penny & dime was from "Dreamland I & II", the dog tag was from her dog she got in "Clyde Bruckman's Final Repose".

Dr. Stites had been reading ''The Sixth Extinction: Patterns of Life and the Future of Mankind'' by Richard Leakey and Roger Lewin. The title of the book provides a reference to the title of the first episode of the seventh season.

Quotes:
Doggett: Agent Scully. Can I take your coat?
Scully: I'm not staying, Agent Doggett. My doctor told me to take my maternity leave, in fact, she insisted on it.
Doggett: That's not bad, Agent Scully, you could use some time for yourself. What is it?
Scully: It's a medallion commemorating the Apollo 11 space flight. I'd like to give this to you, Agent Doggett.
Doggett: Thanks. Because?
Scully: Agent Mulder gave it to me a few years back. It symbolises teamwork, partnership... it means no one gets there alone. And after this past year and... everything that we've been through, I just... I wouldn't be here without you. (She hugs Doggett)
Doggett: Agent Scully, this pregnancy leave, it is just a leave right? I mean, you are coming back eventually? (She smiles and leaves the office. Doggett looks around the office shaking his head, he smiles as he hears the sound of woman's shoes in the hallway) You're not gone five minutes, Agent Scully and I already I'm starting to feel like a stranger in my own off ..." (It isn't Scully standing in the doorway)
Agent Harrison: I'm sorry?
Doggett: Can I help you?
Agent Harrison: I'm here to help you, actually. I'm Leyla Harrison. I've been looking forward to meeting you.
Doggett: Uh huh.
Agent Harrison: I've got a case here, an X-File, I think. At least the local PD can't explain it. A murder last night in upstate New York. I booked us on a flight to Buffalo Niagara. Here's the crime report.
Doggett: I'm sorry, Miss Harrison, who are you?
Agent Harrison: Oh gosh, they didn't tell you? This is so embarrassing — I'm... I'm your new partner.

Agent Harrison: I gave the slime to the Buffalo PD. I told them we wanted to see the results right away.

Doggett: How much field experience do you have, Agent Harrison?
Agent Harrison: Um, actually this is my first time in the field.
Doggett: Let me guess, Deputy Director Kersh handed you this job, filling in for Agent Scully.
Agent Harrison: Yes. Yes he did.
Doggett: I don't know how to tell you this, Agent Harrison, but you're being used. Deputy Director Kersh is no friend to the X-Files.
Agent Harrison: I don't think you understand something, Agent Doggett. I begged for this assignment.
Doggett: You begged for it?
Agent Harrison: I was in accounting. I processed Agents Mulder and Scully's travel expenses.
Doggett: Then you are qualified.
Agent Harrison: Maybe I'm not. But I know the X-Files, Agent Doggett, inside and out. Other people don't even want to admit these questions exist, but you face them every day. I am just so excited to be a part of this. Aren't you? Mr Sacks' body was found here, but they found no foot prints leading to it. Oh my god. There's more of it.
Doggett: Looks like it.
Agent Harrison: You know what that could be? It could be bile.
Doggett: Bile?
Agent Harrison: From a liver-eating mutant. Mulder and Scully chased one into an escalator once. It died, but there was...
Doggett: This is not a liver-eating mutant, Agent Harrison.
Agent Harrison: It could be an alien who send its skin. According to Agent Mulder's case reports they leave behind a mucous-like residue when they... You don't think it's that either. I'll take a sample of this, have it sent to the lab for comparison.
Doggett: That's good thinking, Agent Harrison.

Mulder: Seems like old times. You in scrubs, slicing and dicing.

Scully: What are you doing here, Mulder?
Mulder: Actually, I wandered away from my tour. A better question is; what are you doing here?
Scully: I found something that may prove helpful in locating Agent Doggett. This is Arlen Sacks, the murder victim Doggett was investigating. This old man was not murdered, Mulder. He died of heart failure, evidently after he was blinded by a chemical substance of some kind. The orbits have residual traces of a slimy substance, known as hydrolytic enzymes.
Mulder: Venom. Produced by reptiles.
Scully: How'd you know that?
Mulder: Before Agent Doggett and his partner went missing, they send in samples to be analysed — hydrolytic enzymes. Skinner told me.
Scully: I also found some bacteria in the venom, which I'm going to do a culture on.
Mulder: Let someone else do it. There are other concerns right now.
Scully: I know. But this is an X-File, Mulder and you are out of the Bureau. And now If I go home, where is Skinner going to find someone qualified to look into this?
Mulder: I know where he could find somebody.

Agent Harrison: This means... I can't tell you what this means to me. Can I ask you something?

Mulder: Sure.
Agent Harrison: When you went to Antarctica, to save Agent Scully from being taken by that spaceship, and you ran out of gas in your snowcat, how did you get back?
Scully: Um, well first of all it was never... actually proven that it was a spaceship.
Mulder: It wasn't?
Scully: Well, no, what...
Mulder: Proven?
Scully: What happened was that we fell off of something that...
Mulder: Something?
Scully: ...rose out of the ice.
Mulder: Well, what do you think that was?
Scully: Well, I don't know what it was, but we never, we didn't actually see...
Mulder: Was it a spaceship?
Scully: ...a spaceship.
Mulder: I can't believe you're saying it's not a spaceship, when you saw it.
Scully: Ah, I mean, it could have been a spaceship. Mulder, but you don't...
Mulder: Of course it was a spaceship.
Scully: Look, we don't know that it was, but you don't have a picture of it or anything.
Mulder: You know it was a spaceship, you saw it!
Scully: No, I did, no no no no no. Remember, I was unconscious. And when I woke up there was no spaceship.
Mulder: You saw the spaceship.
Scully: No no no.

Episode Number: 180
Season Number: 8
First Aired: Sunday, May 6, 2001
Production Code: 8X19