Parts of the set for Marita Covarrubias's NYC apartment were reused/redressed from the episode "The Field Where I Died." You can see the distinctive leaded glass design in both episodes.
Krycek: You're keeping me in the dark?
Mulder: (punches Krycek) Yeah
Mulder: I don't speak Russian.
Prisoner: Then no one told you.
Mulder: Told me what?
Prisoner: That you were brought here to die. To wish you were dead.
Mulder: I wasn't brought here, I came here looking for something
Prisoner: The only thing you will find here is death.
Mulder: What is this Place?
Prisoner: This Place.. A Gulag, a place where the guilty rule the innocent.
Scientist: (To Mulder and Scully) This rock contains what are called Polythiclicaromatic Hydrocarbons fitting the approximate description of those in fragments of meteorite found recently in the ice fields of Antarctica.
Krycek: Hey, you go underground, you gotta learn to live with the rats.
Mulder: I'm sure you had no trouble adapting.
Mulder: (to Krycek) You're an invertebrate scum sucker whose moral dipstick is about two inches short of bone dry.
Scully: What I'm worried about is you, Mulder. How far you'll go... and how far I can follow you.
Scully: You want this man brought to justice?
Krycek: You can't bring these men to justice. They're protected. The laws of this country protect them in the name of national security. They know no law.
Mulder: Then why don't you put a bullet in his head like you did that man out there?
Krycek: These men, they fear one thing; exposure. You expose *him,* you expose his crimes, you destroy the destroyer's ability to destroy.
Mulder: The only thing that will destroy this man is the truth.
Krycek: The truth, the truth! There's no truth. These men, they make it up as they go along. They're the engineers of the future. They're the real revolutionaries.
The character of Dr. Sacks (the scientist who is infected by the Black Cancer in the rock) is possibly named after the famed neurologist Oliver Sacks, whose book "An Anthropologist On Mars" was a major influence on the episode "Demons".
In the closed captioning for this episode, viewers saw Mulder pull a cockroach out of a drinking cup and say: "Bambi?". This is a reference Dr. Bambi Berenbaum, an entomologist studying cockroaches who appeared in the season 3 episode 'War of the Coprophages'.
Krycek tells Mulder that "When you go underground you gotta learn to live with the rats", a possible reference to Nick Lea's nickname, 'Ratboy'.
Mulder: What did you get for trick or treat, Charlie Brown?
This is a reference to the perennial TV animated special It's The Great Pumpkin, Charlie Brown. In that cartoon, as the kids compare what they get from each house, all Charlie Brown can say is, "I got a rock."
Tunguska is the location in Siberia where an object (asteroid? UFO?) struck the earth on June 30, 1908. The blast levelled over a half million acres and was hundreds of times stronger than the blast of the atomic bomb dropped on Hiroshima.