Mulder: How was the opera?
X: Wonderful. I've never slept better.

Mulder: I could be mistaken. Maybe it was another bald-headed, jigsaw-puzzle-tattooed, naked guy I saw.

Mulder: I got the impression that Glazebrook wasn't the only sideshow performer residing here.

Mulder: I'm going to find Trepkos.
Scully: What if he's already dead?
Mulder: Then he'll have a lot of trouble answering my questions.

Mulder: I've always figured that dreams are answers to questions we haven't figured out how to ask yet.

Mulder: My father's dead, Scully. They killed him.
Season 3

Mulder: People videotape police beatings on darkened streets. They manage to spot Elvis in three cities across America every day, but no one saw a pretty woman forced off the road in a rental car.

Mulder: So... lunch?
Scully: Mulder, toads just fell from the sky!
Mulder: I guess their parachutes didn't open. You were saying something about this place not feeling "odd"?

Mulder: Tell me, have you done much circus work in your life?
Mr. Nut: And what makes you think I've ever spectated a circus? Much less been enslaved by one?
Mulder: I know that many of the citizens here are former circus hands, and I just thought that...
Mr. Nut: 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 would it have occurred to you that a person of my height could have possibly obtained a degree in Hotel Management.
Mulder: I'm sorry. I meant no offence.
Mr. Nut: Well then why should I take offence? Just because it's human nature to make instantaneous judgements of others based solely upon their physical appearances? Why I've done the same thing to you, for example. I've taken in your all-American features, your dour demeanour, 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 deduced you to a stereotype. A caricature, instead of regarding you as a specific, unique individual.
Mulder: But I am an FBI agent.

Salvatore Matola: They said it'd be like living two lifetimes. At- at first, that's what it was like. Not having to sleep at all made us feel like nothin' could touch us, you know? We'd do 24 hour patrols, night ambushes, you know, and that type of thing.
Mulder: And you never got tired?
Salvatore Matola: No. Not so that we had to sleep. And then, nothing that the pills couldn't fix.
Mulder: Serotonin?
Salvatore Matola: Yeah.
Mulder: How long did this go on?
Salvatore Matola: Quite a while, I'd say. Quite a while - until we stopped taking orders from the company commander in Saigon.
Krycek: You mean the entire squad went AWOL?
Salvatore Matola: Yeah, somethin' like that.
Mulder: Well, then who did you take orders from?
Salvatore Matola: We just made up missions as we went along, until it didn't matter anymore who we were killing. Farmers, women. Outside of Phu Bai, there was this school...they were just kids.

Scully: According to the briefing, the prisoners escaped while hiding in a laundry cart.
Mulder: I don't think the guards have been watching enough prison movies.

Scully: Neat trick, Mulder; for your birthday I'll buy you a utility belt.

Scully: Somebody shoved this under my door. I guess you really do have a friend in the FBI. And, Mulder, when you see Skinner to hand in field report, I hope that you know that I'd consider it more than a professional loss if you decided to leave.

Scully: There's no sign of him, Mulder. Maybe he's moved on. What are you looking at?
Mulder: On the videotape, Dr. Banton kept staring at the floor. I've been trying to figure out what he might have been looking at.
Scully: Well, maybe the exposure affected his mind. Nonsensical repetitive behavior is a common trait of mental illness.
Mulder: You trying to tell me something?

Scully: (Scully reads her report on the case as a voiceover as she enters Mulder's hospital room and sits down next to him.) Transfusions and a treatment with antiviral 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, but this uncertainty has only strengthened my need to know, to understand, to apply reason to those things that 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.