Scully: Mulder, there are thousands of scientists working on the Human Genome project.
Mulder: Yeah, but only one who decided to go bungee jumping with medical gauze wrapped around his neck.
Season 2

Scully: Must be for the visually impaired.
Mulder: How do you like that? A politically correct elevator.

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

Scully: Okay, Mulder. But I'm warning you, if this is monkey pee, you're on your own.

Scully: So, how do I die?
Clyde Bruckman: You don't

Scully: So, what are we supposed to charge him with, 'assaulting a cellular phone'?

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: The 65-year-old female teller was pistol-whipped. Died from a massive subdural hemorrhage all because she didn't put the money in the bag fast enough.
Mulder: Lovely couple.

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: What are you going to do?
Mulder: I know what I'm not going to do. I'm not going to hang around and wait for Barnett to send me another valentine.

Scully: What do you think?
Mulder: I think I'm going to suggest we sleep with the lights on.

Scully: Who is this "Deep Throat" character? I mean, we don't know anything about him. What his name is, what he does...
Mulder: He's in a delicate position. He has access to information and indiscretion could expose him.
Scully: You don't know that this isn't just a game with him. He's toying with you. Rationing out the facts.
Mulder: You think he does it because he gets off on it?
Scully: No. I think he does it because you do.

Scully: You've got that look on your face, Mulder.
Mulder: What look is that?
Scully: The kind when you've forgotten your keys and you're trying to figure out how to get back in the house.

Scully (to Mulder): Please explain to me the scientific nature of the "whammy".

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.