JEREMIAH SMITH: You have to understand something. I must perish. Whatever the consequences to that end, they are incalculable to the preservation of the larger plan.
MULDER: The larger plan? You mean colonization.
JEREMIAH SMITH: Hegemony, Mister Mulder. A new origin of species.
JEREMIAH SMITH: You're looking at the future, Mister Mulder.
MULDER: What is it?
JEREMIAH SMITH: A flowering shrub. But it's specific epithet can't be found in any of your taxonomic charts.
MULDER: Being grown for what?
JEREMIAH SMITH: Pollen.
MULDER: What is this? What's going on here?
JEREMIAH SMITH: What did I tell you, Mister Mulder?
MULDER: That looks just like my sister. But that's not possible. She's no older than the day she was taken.
SCULLY: Not until you give me some information first. These are data entries taken from social security records...
X: You're going in the wrong direction, Agent Scully.
SCULLY: All beginning with the letters S-E-P. You know what these are. Confirm or deny.
X: Smallpox eradication program.
X: Don't unlock doors you're not prepared to go through, Agent Scully.
SCULLY: "SEP." Smallpox Eradication Program.
PENDRELL: Smallpox? How'd you figure that?
SCULLY: I got lucky, but the key is in this first string of letters.
PENDRELL: Twenty-letter strings. Thirty different variations.
SCULLY: You say "a twenty-letter code" to any scientist, and they immediately think "protein amino acid sequence..." which is what this turned out to be.
SECOND SENIOR AGENT: With all due respect, Agent Scully... it looks like something from the Hubble telescope.
SCULLY: Actually, it's an image created by what's called a confocal microscope. You're looking at a three-dimensional picture of the location of a protein. In this case, cowpox structural protein number six. It's one of the inoculants used in smallpox vaccines.
SENIOR FBI AGENT: Where'd it come from?
SCULLY: From me. I had a biopsy taken from the smallpox vaccination scar on my upper arm. Through a process called immunohisto chemical staining and through the addition of an antibody for the cowpox virus six, I was able to get this picture of the location of a protein... a single, non-random, protein pattern.
SKINNER: I'm not a scientist, Agent Scully, and I don't know that many people in this room...
SCULLY: What I'm saying is that I think this protein is a tag... some kind of genetic marker that was applied to me when I was inoculated against smallpox as a child.
SKINNER: Do you realize what you're promoting in there? You're rounding these people up in the middle of the work day to imply that there's...
SCULLY: I am a scientist, sir. What I'm promoting in there is reductive evidence. It's the reason I believe I was assigned to the X-Files in the first place, is it not? To put Agent Mulder's work to the test of science?
ALIEN BOUNTY HUNTER: He shows you pieces, but tells you nothing of the whole... because he's inconsequential... a traitor to the project.
MULDER: Kill me, let them go.
ALIEN BOUNTY HUNTER: You'd trade your life for his?
MULDER: For my mother's.
ALIEN BOUNTY HUNTER: Everything dies.
MULDER: I've seen too many things not to believe.
SCULLY: I've seen things too. But there are answers to be found now. We have hope that there's a place to start. That's what I believe.
MULDER: You put such faith in your science, Scully. But... the things I've seen, science provides no place to start.
SCULLY: Nothing happens in contradiction to nature, only in contradiction to what we know of it. And that's a place to start. That's where the hope is.
COVARRUBIAS: Not everything dies, Mister Mulder.
ALIEN BOUNTY HUNTER: I need to know the reasons why this should be.
CIGARETTE-SMOKING MAN: So that the work may continue. So that the project may proceed unabated by removing an unnecessary obstacle.
ALIEN BOUNTY HUNTER: What obstacle?
CIGARETTE-SMOKING MAN: Agent Mulder, actually. If his mother were to die, he would...
ALIEN BOUNTY HUNTER: He what?
CIGARETTE-SMOKING MAN: You see... the fiercest enemy is the man who has nothing left to lose. And we both know how valuable Agent Mulder is to the equation.