CIAB: Conversation in the Autopsy Bay, Sleepless
(Scully’s autopsy bay. She places a large organ on the scale.)

Mulder: Spleen or pancreas?
Scully: (She flashes a smile at him.) Stomach. I was just about to start on it. (Her smile turns into a grim line when she sees Alex Krycek come in.)
Mulder: This is Alex Krycek. We're, uh, working the case together.
Scully: Good to meet you. (Nods at him, slightly)
Krycek: You, too. (He holds out his hand, she walks right by it.)
Scully: Notice the pugilistic attitude of the corpse. (Krycek coughs into fist, loudly. Scully looks pointedly at Mulder. Mulder rolls his eyes heavenward as if to say- 'yeah, he's green all right.' When Scully starts to speak again, it's in a much softer voice. As she continues she becomes quieter, and quieter, until she is almost whispering by the end of the scene.) This condition generally occurs several hours after death. It's caused by a coagulation of muscle proteins when the body is exposed to extremely high temperatures.
Mulder: Like fire?
Scully: This degree of limb flexion is observed exclusively in burn related victims.
Krycek: But there was no fire. (I'm amazed he could even hear this!)
Scully: And no epidermal burns to indicate as much but when I opened up the skull, I found external hemorrhages, which can only be caused by intense heat. Somehow, this man suffered all of the secondary, but none of the primary physiological signs of being in a fire.
Mulder: Any theories?
Scully: I couldn't even begin to explain what could have caused this. It's almost as if. . .
Mulder: What?
Scully: It's almost as if his body believed that it was burning.

Comments: What can I say? Even if you're not a 'shipper' this scene is still great, because Mulder and Scully belong together as partners. Scully is obviously showing a wide streak of jealously here, but Mulder's playing it up, as he moves in close to Scully with his back to Krycek, effectively shutting him out of the conversation.
 

COTP: Conversation on the Phone, Sleepless

(Scully is writing up her finding concerning the sleep eradication program when Mulder calls.)

Scully: Scully
Mulder: Well, that second officer is still in a coma, so I don't think we can count on him to give us an answer.
Scully: I'm going over these reports you faxed me. They're incredible.
Mulder: Well, the military already sent troops to radioactive mushroom clouds, I guess they figured they had to top themselves, right?
Scully: Sleep eradication still doesn't explain the shooting of those two officers, or the anomalous autopsy results on Willig and Dr. Grissom.
Mulder: Well, I learned something at Dr. Grissom’s clinic. About what happens to a persons cortex when you stimulate it with electricity.
Scully: They experience mild visual and auditory hallucinations, any first year med. student could tell you that.
Mulder: Well, what if that stimulus were to come from a remote source? What if Cole had somehow developed the ability to project his unconscious?
Scully: Are you suggesting that Cole killed these people with telepathic images?
Mulder: Think about it, Scully. In all those years without REM sleep, maybe Cole built a bridge between the waking world and the dream world. A collective unconscious. And what if, by existing consciously in the unconscious world, he developed the ability to externalize his dreams and effectively alter reality.
Scully: Even if you're right, you'll have a much better chance of finding Cole if you work up a profile and try to surmise his next move.
Mulder: All right, I'll sharpen my pencils and I’ll see you later. (Look ma, he's actually listening to Scully!) (Krycek beckons towards Mulder.) I’ll be right there, Krycek.
Scully: Where are you going?
Mulder: We're gonna check out another member of the squad and see if he can tell us anything about Cole.
Scully: (With a wistful look on her face.) Sounds like your new partner's working out.
Mulder: He's all right. He could use a little more seasoning and some wardrobe advice. But he's a lot more open to extreme possibilities then. . .
Scully: Then I was?
Mulder: . . .then I assumed he would be.
Scully: Must be nice not having someone question your every move, poking holes in all your theories.
Mulder: Oh yeah, it’s---it’s great. I'm surprised I put up with you so long.
Scully: You'd better go. I’ll read over this report again and see what else I can come up with.
Mulder: Okay. (Hangs up phone.)

Irresistible

Scene in Mrs. Pfaster's house, Irresistible

(Scully has been abducted by Donnie Phaster. He has cut the bonds he had around her feet and brings her into the bathroom. He has prepared a tub of cold water. Scully backs away, trying to escape. Donnie moves towards Scully, grabs her, but she pushes him hard straight into the freezing water in the bathtub. Scully then rushes out of the bathroom. Donnie pulls himself, wet, from the tub, and starts chasing her. He walks out of the bathroom, and looks around. Scully has disappeared. He's moving around the house, looking for her. Scully reaches the front door. It's locked. She runs for a place to hide.)

Donnie: There's no way out, girlie girl. (enters a bedroom, and retrieves a gun from the dresser) I know this house, girlie girl. There's nowhere to hide.

(He then hears a noise from one of the rooms, and rushes in that direction. He moves towards a closed door and opens it. Scully jumps forward, her gag removed, with a spray bottle in her tied hands. She sprays him in the eyes, and runs off, while he's stumbling backwards. Scully runs towards the staircase, Donnie after her. He catches her at the top of the stairs, and they both tumble down the staircase. As they hit the floor, Donnie's gun slips out of his grasp. Scully starts crawling for the gun, Donnie sees her, and leaps on top of her. As she's pointing the gun at him, she, again, sees the demon from her dream, which shocks her, and allows Donnie to snap the gun from her hands. At that moment, the door bursts open, Mulder, Bocks and a few officers rush in.)

Mulder (gun brandished): FEDERAL AGENTS! HANDS IN THE AIR!

(Donnie slowly puts his hands in the air, and the other men take him forcefully. Mulder kneels down to Scully. She's dazed, as she's trying to get up.)

Mulder (loudly): Let's get the paramedics out here!
Scully: I'm okay.
Mulder: Just stay there, Scully.
Scully (she insists on getting up, Mulder helps her): I'm fine. Just help me get my wrists undone. (As Mulder starts untying her) How did you find me?
Mulder: His Mother used to own the house, willed it to the sisters. I played a hunch. A patrolman spotted the car out front.
(Her wrists untied, Scully rubs them. She doesn't want to meet Mulder's eyes. She's looking over at Donnie, who's being bound on the floor.) Why don't you sit down until someone can take a look at you.
Scully (quietly): Mulder, I'm fine.

(Mulder looks at her, and tips up her chin. She, then, meets his gaze, and that's all it takes. Her eyes well up, and she lets out a huge sob. Mulder's holding her now, though she keeps her arms crossed in front of herself. She, then, allows herself to hold him, to fully let her emotions out. Scully continues to cry in Mulder's arms, while he holds her tight and strong.)

End Game

(Emergency Room; Eisenhower Field. Scully bursts into the emergency room. Mulder is sitting in a tub, an oxygen mask on. The people are talking in the background.)

Nurse: No change in B.P. or pulse.
Scully: (Scully looks at Mulder and holds up her badge.) I'm Dana Scully, I'm Agent Mulder's partner. What are his vitals?
Doctor: (He walks over to her.) He's suffering from extreme hypothermia.
Scully: No... you've got to get him out of the tub.
Doctor: He's dying, he's lost all his body heat.
Scully: You've got to listen to me! If you keep him in there, you're going to kill him! The cold is the only thing that's keeping him alive. (Mulder flatlines.)
Nurse: His heart stopped!
Doctor: Give me one amp of epinephrine in a canyon tube!
Scully: You don't know what you're dealing with here! Agent Mulder has been exposed to a retrovirus resulting in hyperviscosity syndrome.
Doctor: I want you out of my E.R. right now. Nurse! (A nurse walks over to her.)
Nurse: Yes, doctor. Ma'am...
Scully: His blood has thickened...
Nurse: Ma'am...
Scully: That's why his heart is failing!
Doctor: (He spins around.) No, his heart is failing because he's lost all his body heat!
Scully: No, the only thing saving him right now is the hypermetabolic state induced by the cold. Now, if you don't do what I'm saying, you are going to kill him! (I gotta tell you, although Scully is somewhat ruffled here, she's still pretty calm. Me- I'd have been screaming and yelling at this point!) (The doctor stares at her for a second. She takes off her coat.) Let's get him out of that tub now.

(The doctor holds an oxygen mask over Mulder's mouth as Scully readies the defibrillators.)

Man: A hundred joules, charged and ready.
Scully: Clear!
Woman: Clear. (Scully puts the defibrillators down on Mulder's chest and they go off. Still no pulse.) No rhythm.
Man: Charge?
Doctor: No.
Scully: Clear!
Woman: Clear. (Scully tries again. A slight pulse picks up.)
Doctor: I'm picking up a faint pulse.
Scully: (Scully puts the defribillators down.) I want a digoxin 0.1 milligram I.V. Hang a heparin drip at 1,000 units per hour. And get him two units of fresh frozen plasma now. (The nurse runs off to do so.)
Doctor: This patient's not even in...
Scully: He's going to make it. (She runs her hand through his hair.)
Man: Let's get the plasma going. Okay, let's get a second line ready.
Other Man: Push the adrenaline...

(Later, Mulder lays on his hospital bed, oxygen tube in his nose. Scully sits at his bedside. We hear her voice over the scene.)

Scully: Transfusions and an aggressive treatment with anti-viral agents have resulted in a steady but gradual improvement in Agent Mulder's condition. Blood tests have confirmed his exposure to the still unidentified retrovirus whose origin remains a mystery. The search team that found Agent Mulder has located neither the missing submarine nor the man he was looking for. Several aspects of this case remain unexplained, suggesting the possibility of paranormal phenomena... but I am convinced that to accept such conclusions is to abandon all hope of understanding the scientific events behind them. Many of the things I have seen have challenged my faith and my belief in an ordered universe...

(Later, a nurse opens the door to Mulder's room for Scully, who sits down at his bedside. He no longer has the oxygen tube and is looking much healthier than before. Scully places both hands on her partner's arm.)

...but this uncertainty has only strengthened my need to know, to understand, to apply reason to those things which seem to defy it. It was science that isolated the retrovirus Agent Mulder was exposed to, and science that allowed us to understand its behavior. And ultimately, it was science that saved Agent Mulder's life. (Mulder groans. Scully looks up at him and smiles. He slowly turns to look at her.) Hey. How you feeling?
Mulder: (In a whisper.) Like I got a bad case of freezer burn. How did I get here?
Scully: A naval reconnaissance squad found and choppered you to Eisenhower Field. (He nods.) Thanks for ditching me.
Mulder: I... I'm sorry, I... I couldn't let you risk your life on this.
Scully: Did you find what you were looking for?
Mulder: No. No. But I... I found something I thought I'd lost. Faith to keep looking. (She smiles.)

Humbug

CBM&MN: Conversation between Mulder and Mr. Nutt, Humbug

Mr Nutt: You thought that because I am a person of short stature, that the only career I could procure for myself would be one confined to the so-called Big Top. You took one quick look at me, and decided that you could deduce my entire life. Never did it occur to you that a person of my height could have possibly obtained a degree in Hotel Management.
Mulder: I'm sorry. I meant no offense.
Mr Nutt: Well then why should I take offense? Just because it's human nature to make instantaneous judgments of others based solely upon their physical appearances? Well I've done the same thing to you, for example. I've taken in your all-American features, your dour demeanor, your unimaginative necktie design, and concluded that you work for the government, an FBI agent. But do you see the tragedy here? I have mistakenly reduced you to a stereotype. A caricature, instead of regarding you as a specific, unique individual.
Mulder: But I am an FBI agent.

Comments: This is here, because it is so hysterical. It's an exchange like this that shows what a genius Darin Morgan is.
 

CBS&DB: Conversation between Scully and Doctor Blockhead, Humbug

Scully: Well, his body possesses some anatomical discrepancies ... some offshoots of the esophagus and trachea that almost seem umbilical in nature and... I've never seen anything like it.
Blockhead: And you never will again. Twenty-first century genetic engineering will not only eradicate the siamese twins and the alligator skinned people, but you're going to be hard pressed to find, uh, a slight overbite or a not-so-high cheek bone. You see, I've seen the future and the future looks just like him. (He points at Mulder, who is standing in front of a trailer in a classic model pose. Hands on his hips, one foot up on the step, looking off into the distance.) Imagine going through your whole life looking like that. That's why it's left up to the self-made freaks like me and the Conundrum to remind people.
Scully: Remind people of what?
Blockhead: Nature abhors normality. It can't go very long without creating a mutant. Do you know why?
Scully: No, why?
Blockhead: I don't either, it's a mystery. Maybe some mysteries are never meant to be solved.

Anasazi

CITM: Conversation in Mulder's Apartment, Anasazi

(Mulder is sleeping in his apartment - someone is walking toward him. He wakes up and reaches for his gun... )

Scully: You didn't answer your door.
Mulder: Oh. I took a pill.
Scully: I couldn't find you at work. I was worried about you.
Mulder: I came home. I must be running a fever. Maybe it's the threat of being burnt at the stake.
Scully: They called me in today.
Mulder: What did you tell them?
Scully: That nothing was wrong.
Mulder: Well, you told them the truth then.
Scully: Mulder, you opened the door for them, they're just looking for a good reason now.
Mulder: Okay, I'll say I'm sorry.
Scully: Mulder, these files. Who knows you have them?
Mulder: Why?
Scully: Because I had to lie today. And I put my job in jeopardy in order to do so. If they find out about those files...
Mulder: How would they find out?
Scully: Maybe they already know. The question is, is it worth it? Is this cassette worth risking everything?
Mulder: I'll tell you when I find out what's on it. (Yells) Now just tell me who I can talk to about breaking that code.
Scully: (Somewhat taken aback.) I'm meeting with someone in an hour. I might know something later tonight, I just need some kind of assurance that they're not going to let us hang ourselves with this. That I'm doing the right thing.
Mulder: (Calmer) I'll try to find out. (Mulder tapes an X to the window... )
Scully: I need to know one more thing Mulder. Why did you attack Skinner?
Mulder: I've thought of that Scully. I honestly can't say.

Comments: Tense scene. Mulder's behavior is very erratic, and Scully has lied to protect her partner. The lies don't sit well with her. Then, Mulder just about takes her head off. He could try the patience of a saint (which she is <g>.) Still, she doesn't give up on him. Although by the end of the scene you can almost hear her thinking. ' You know why- but are unable to tell me or you don't know why you acted this way?'
 

Scene where Scully shoots Mulder, Anasazi

( Scully is at Mulder's apartment gathering evidence. Outside, Mulder gets out of a cab and sees someone go around the side of the building. He runs through the building to the other side.  Mulder grabs the person as he walks around the corner, and then punches him - it's Krycek...)

Mulder: I'm gonna kill you anyway, Krycek, so you may as well tell me the truth. Did you kill my father? Did you kill him ... answer me! ( Mulder punches him ).
Scully: Mulder, don't shoot him. Just back away. (Scully points a gun at Mulder... )
Mulder: He killed my father, Scully.
Scully: I have him, Mulder.
Mulder: No, Scully... ( He starts to squeeze the trigger and...Scully shoots Mulder, Krycek runs off.)
Woman's Voice: Oh my God.  Somebody call the police.