Mulder and Scully must fight the government in a conspiracy and find the truth about an alien colonization of Earth.

Special Agent Dana Scully: I need this building evacuated and cleared out in ten minutes. I need you to get on the phone and tell the fire department to block off the city center in a one mile radius around the building. DON'T THINK! JUST PICK UP THE PHONE AND MAKE IT HAPPEN!
Special Agent Fox Mulder: [Mulder and Scully are attempting to follow a truck] I think they went left.
Special Agent Dana Scully: I don't know why, I think they went right.
Special Agent Fox Mulder: [Mulder impulsively guns it and takes off straight ahead] Five years together, Scully. How many times have I been wrong? Never!
Special Agent Fox Mulder: [He looks at her and amends:] Not driving, anyway.
Special Agent Dana Scully: Any thoughts as to why anybody would be growing corn in the middle of the desert?
Special Agent Fox Mulder: Those could be giant Jiffy-Pop poppers.
Well-Manicured Man: You have precious little time, Agent Mulder. What I have given you to save Agent Scully, the alien colonists living amongst us do not yet know exists. It's introduction into an alien environment may have the capability to destroy all the delicate plans to fight the alien re-colonization of Earth that we have so delicately protected for the last 50 years.
Special Agent Fox Mulder: What do you mean "may have"?
Well-Manicured Man: Find Agent Scully. Only then you will know the grand scope of things.
Special Agent Dana Scully: Mulder what are you doing?
Special Agent Fox Mulder: Something's wrong!
Special Agent Dana Scully: Mulder!
Special Agent Fox Mulder: Something's not right!
Special Agent Dana Scully: Mulder get in the car! THERE'S NO TIME!
Special Agent Dana Scully: [Mulder revives Scully by performing CPR] I had you big time.
[to a bartender, while drinking]
Special Agent Fox Mulder: I'm the key figure in an ongoing government charade, the plot to conceal the truth about the existence of extraterrestrials. It's a global conspiracy, actually, with key players in the highest levels of power, that reaches down into the lives of every man, woman, and child on this planet, so, of course, no one believes me. I'm an annoyance to my superiors, a joke to my peers. They call me Spooky. Spooky Mulder, whose sister was abducted by aliens when he was just a kid and who now chases after little green men with a badge and a gun, shouting to the heavens or to anyone who will listen that the fix is in, that the sky is falling and when it hits it's gonna be the shit-storm of all time.
Barmaid: [backs away] Well... I say that about does it, Spooky.
Special Agent Fox Mulder: [shakes his head with disbelief] Well... I guess you're right. How much do I owe you for all these drinks?
Barmaid: 86 is your lucky number... Spooky.
Special Agent Fox Mulder: [beat] No. My lucky number is one.
Special Agent Fox Mulder: How many times have we been here before, Scully? Right here. So close to the truth and now with what we've seen and what we know to be right back at the beginning with nothing.
Special Agent Dana Scully: This is different, Mulder.
Special Agent Fox Mulder: No, it isn't! You were right to want to quit! You were right to want to leave me! You should get as far away from me as you can! I'm not gonna watch you die, Scully, because of some hallow personal cause of mine. Go be a doctor. Go be a doctor while you still can.
Special Agent Dana Scully: I can't. I won't. Mulder, I'll be a doctor, but my work is here with you now. That virus that I was exposed to, it has a cure. You held it in your hand. How many other lives can we save?
[clasps Mulder's hand]
Special Agent Dana Scully: Look... if I quit now, they win.
Special Agent Fox Mulder: Whatever happened to playing a hunch, Scully? The element of surprise, random acts of unpredictability? If we fail to anticipate the unforeseen or expect the unexpected in a universe of infinite possibilities, we may find ourselves at the mercy of anyone or anything that cannot be programmed, categorized or easily referenced.
[Pops a sunflower seed into his mouth]
Special Agent Fox Mulder: What are we doing up here, Scully? It's hotter than hell.
Special Agent Dana Scully: Are you drunk, Mulder?
Special Agent Fox Mulder: I was until about 20 minutes ago.
Special Agent Dana Scully: Was that before or after you decided to come here?
Special Agent Dana Scully: I saw your face, Mulder. There was a definite moment of panic.
Special Agent Fox Mulder: You've never seen me panic. When I panic, I make this face.
[remains impassive]
Special Agent Fox Mulder: [looking at a vile of serum with a syringe] What's this?
Well-Manicured Man: A weak vaccine against the virus Agent Scully has been infected with. It must be administrated within 96 hours after first contact or she will be beyond saving.
Special Agent Fox Mulder: A virus?
Well-Manicured Man: What is a virus, Mr. Mulder? A rare certain strain of Purity that has been lying dormant in a cave in Texas since the end of the last great Ice Age waiting to be unleashed upon this world?
Special Agent Fox Mulder: Is this what you and your consortium have been covering up all this time? A virus? A disease?
Well-Manicured Man: No, no, no, you've got it all backwards! AIDS, the Ebola virus, the common cold... on an evolutionary scale they are newborns. This virus walked the Earth long before the first dinosaurs appeared.
Special Agent Fox Mulder: What do you mean "walked"?
Well-Manicured Man: Your aliens, Agent Mulder, your little green men arrived here millions of years ago.
Special Agent Dana Scully: [after tricking Mulder into the door being locked] I had you.
Special Agent Fox Mulder: No, you didn't.
Special Agent Dana Scully: Oh, yeah. I had you big time.
[last lines]
Conrad Strughold: Oh, you look hot and miserable. Why have you traveled all this way?
Cigarette Smoking Man: We have business to discuss.
Conrad Strughold: You have regular channels.
Cigarette Smoking Man: This involves Mulder.
Conrad Strughold: Ah, that name. Again and again.
Cigarette Smoking Man: He's seen more than he should.
Conrad Strughold: What has he seen? Of the whole, he has seen but pieces.
Cigarette Smoking Man: He's determined now, reinvested.
Conrad Strughold: He's but one man. One man alone cannot fight the future.
Cigarette Smoking Man: Yesterday, I received this.
[hands him a telegram]
Conrad Strughold: [reads it, then drops it with a worried look] Oh...
[we see that it reads: "X-Files reopened. Stop. Please advise. Stop"]
Special Agent Fox Mulder: [after Scully tells him that she is planning on resigning from the FBI rather than being transferred] You wanna tell yourself that so you can quit with a clear conscience, you can, but you're wrong!
Special Agent Dana Scully: Why did they assign me to you in the first place, Mulder? To debunk your work, to rein you in, to shut you down...
Special Agent Fox Mulder: But you saved me! As difficult and as frustrating as it's been sometimes, your goddamned strict rationalism and science have saved me a thousand times over! You've kept me honest. You've made me a whole person. I owe you everything... Scully, and you owe me nothing. I don't know if I wanna do this alone. I don't even know if I can. And if I quit now, they win.
Special Agent Fox Mulder: But you saved me. As difficult and frustrating as it's been sometimes, your God-damned strict rationalism and science have saved me a thousand times over. You kept me honest. You made me a whole person. I owe you everything, and you owe me nothing. I don't know if I want to do this alone. I don't even know if I can.
Well-Manicured Man: Trust no one, Mr. Mulder.
[Scully rings Mulder while he stares at the bomb]
Special Agent Fox Mulder: Remember that face I showed you, Scully? I'm making it again.
[after shooting the driver in the head]
Well-Manicured Man: Get out of the car.
Special Agent Fox Mulder: [expecting to be next] Why? The upholstery is already ruined.
Special Agent Dana Scully: [hands over bee evidence] I don't believe the FBI currently has an investigative unit qualified to pursue the evidence in hand.
Special Agent Dana Scully: Here I am in the middle of nowhere, Texas, chasing phantom tanker trucks.
[on the phone]
Ben Bronschweig, M.D.: It's Bronschweig. Sir, the impossible scenario we never planned for? Well, we better come up with a plan.
Special Agent Fox Mulder: Maybe we should call in a bomb threat to Houston. I think it's free beer night at the Astrodome.
Barmaid: I'd say this about exceeds your minimum daily requirement.
[Mulder knocks over his glass]
Barmaid: Whoa. You've gotta train for that kind of heavy lifting.
Special Agent Fox Mulder: Is this Dr. Kurzweil's residence?
D.C. Cop #1: You got some business with him?
Special Agent Fox Mulder: I'm looking for him.
D.C. Cop #1: Looking for him for what?
[Mulder shows his ID]
D.C. Cop #1: Hey, the Feds are looking for him, too. Real nice business he's got, huh?
Special Agent Fox Mulder: What's that?
D.C. Cop #1: Selling naked pictures of little kids over his computer. You looking for him for some other reason?
Special Agent Fox Mulder: Yeah, I had an appointment for a pelvic examination.
Special Agent Fox Mulder: After all you've seen, you can just walk away?
Special Agent Dana Scully: I have. I did. It's done.
Special Agent Fox Mulder: You told me you had answers.
Alvin Kurtzweil, MD: Yes, but I don't have them all.
Ben Bronschweig, M.D.: [after seeing the formed alien] So much for little green men.
Special Agent Fox Mulder: You know, one is the loneliest number.
[the Cigarette Smoking Man and Dr. Bronschweig climb down a ladder into the cave while wearing bio-haz-mats suits]
Ben Bronschweig, M.D.: We brought the atmosphere back down to freezing in order to control the development of this latest Purity strain... which is nothing like we've ever seen before.
Cigarette Smoking Man: Brought on by what?
Ben Bronschweig, M.D.: Heat, I think. The subsequent invasion of a host, the fireman here, in an enviroment that raised his body temperate above 98.6 degrees.
[they walk into a tent where one of the four firemen infected is laying on a gurney, breathing heavley, near-comatose, his skin black-colored, and hooked up to various I.V. drips]
Cigarette Smoking Man: This man is still alive.
Ben Bronschweig, M.D.: Technicaly and biologicaly... yes. But he'll never recover.
Cigarette Smoking Man: How is this possible?
Ben Bronschweig, M.D.: Look...
[he points to the alien embryo forming in the fireman's chest seen through the skin which is pulsating]
Ben Bronschweig, M.D.: The developing organism is using his life energy. Digesting bone and tissue for itself to grow. We've just slowed the process.
[pause]
Ben Bronschweig, M.D.: You want us to destroy this one too before it jestates?
Cigarette Smoking Man: Uh... no. Not yet. We need to try our vacine on it. We need to see if it will work in this advanced state.
Ben Bronschweig, M.D.: And if it's unsucessfull?
Cigarette Smoking Man: Burn it... like the others.
Assistant Director Walter Skinner: Agent Mulder, you and I both know that if it looks bad, it's bad for the FBI. Blame has to be assigned somewhere.
[Scully is slow to realize a countdown timer signifies a bomb]
Special Agent Fox Mulder: Thirteen fifty-four. Thirteen fifty-two. Thirteen fifty. You see a pattern emerging here, Scully?
Cigarette Smoking Man: Everybody down below! We may have a security breach! If you're not armed, arm yourselves!
Alvin Kurtzweil, MD: And why do you think you're here talking to me today? These people don't make mistakes!
Special Agent Dana Scully: Mulder, I can't tell you what killed this man. I'm not sure if anybody else can, either.
Well-Manicured Man: Survival is the ultimate ideology.
Fire Captain Miles Cooles: [to Bronschwieg] What about my men! What about my men!
Special Agent Fox Mulder: What do you want? Coke, Pepsi, saline IV?