Film: Journey to the Centre of the Earth
The movie that Mulder is watching in his apartment is the 1959 movie Journey to the Centre of the Earth. The movie was directed by Henry Levin and based on the classic novel by Jules Verne.
Goof: Base pairs aren't made up of nucleotides, as the molecular biologist stated, they're as the name states a pair of bases either cytosine and guanine or adenine and thymine in DNA. A DNA nucleotide is a nitrogenous base connected to a sugar (deoxyribose in DNA), a phosphate group and one of the four bases.
Principal setting: Washington D.C.
In the establishing shot of the Fort Marlene facility it is clearly a 2-3 story building. Once Scully gains access and enters the elevator, however, she proceeds to the 7th floor.
Plot Hole: When explaining her findings about the bacteria found in the Purity Control Erlenmeyer, Scully says "they (the bacteria) also contain something that looks like chloroplasts, plant cells". That's not correct, chloroplast is an organelle found inside plant cells and eukaryotic algae that conducts photosynthesis.
Conspiracy Info: We learn the Conspiracy has alien tissue, and is seeking to create an alien/human hybrid.
Plot Hole: On analyzing the bacteria Scully provides, Dr. Carpenter describes the presence of two extra nucleotides and comes to the conclusion that the DNA in question must be extraterrestrial. She overlooks the possibility that it could be artificial.
Continuity: We see that Mulder's apartment has a buzzer to let people in. This buzzer would disappear in later seasons as everybody would just come knocking on agent Mulder's door.
Plot Hole: How did Scully smuggle the alien fetus out of Fort Marlene? The scene leading up to the discovery of the fetus clearly shows that this a very high security facility.
Continuity: In "Colony", we learn that the alien blood is poisonous and will kill the host unless he is chilled very quickly, but Dr. Berube's attic doesn't look very cold.
Deep Throat: Roswell was a smoke screen, we've had half a dozen better salvage operations.
Deep Throat: Trust...trust no one.
Deep Throat: Calling it a night, Mister Mulder?
Mulder: My mother usually likes me home before the streetlights come on.
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.
Mulder: As far as I can tell, he wouldn't pull over for a moving violation.
Scully: Well, that ought to put him in the Ten Most Wanted list.
Dr. Carpenter: Agent Scully.
Scully: Oh, Dr Carpenter, I fell asleep.
Dr. Carpenter: I've done some work. These are the DNA sequences from the bacteria sample you brought in. You seem to know something about molecular biology. Do you know what you're looking at?
Scully: Yeah, I think these are genes.
Dr. Carpenter: Right. They're called base pairs. Each pair is made up of something called a nucleotide. Only four nucleotides exist in DNA, four. And through some miracle of design that we have yet to fathom, every living thing is created out of these four basic building blocks. What you're looking at is a sequence of genes from the bacteria sample. Normally, we'd find no gaps in the sequence. But with these bacteria we do.
Scully: Why is that?
Dr. Carpenter: I don't know why. But I tell you, under any other circumstances my first call would have been to the government.
Scully: What exactly did you find?
Dr. Carpenter: A fifth and sixth DNA nucleotide - - A new base pair. Agent Scully, what you are looking at, it exists nowhere in nature. It, would have to be by definition... extraterrestrial.
(Mulder's cell phone is ringing.)
Crew Cut Man: Your cellular phone's been ringing off the hook.
Mulder: (moaning) I'm a popular guy. Why don't you answer it for me?
Crew Cut Man: Oh, I don't like talking on the phone. I have this thing about unsecured lines. When you feel like talking though, let me know.
(Mulder's cell phone suddenly stops ringing with a suspense tone.)
Scully: Okay, Mulder. But I'm warning you, if this is monkey pee, you're on your own.
Scully: What are you going to do?
Mulder: I'm... not going to give up. Not as long as the truth is out there.
Mulder: It's over Scully.
Mulder: You know, from day one, this has always been on your terms. I've gone along. Been the dutiful son. But maybe this time, we can just cut out the Obi-Wan Kenobi crap and you can save me the trouble.
Deep Throat: I fear you've become too dependent on me.
Mulder: Let me tell you something. I've got plenty to do without chasing down your vague leads or trying to decode your circular logic. Maybe it's you who's become too dependent on me... on my willingness to play your games.
Deep Throat: Mister Mulder?
Deep Throat: Don't give up on this one. Trust me. You've never been closer.
This is the first time we see an alien body.
Ken Kramer, the man who played Dr. Berube, re-appears in the later episode "3" as Dr. Browning.
When Jerry Hardin (Deep Throat) received his copy of the script, a note from series creator Chris Carter was attached to it. The note said: "Nobody ever dies on The X-Files".
The main hallway of Fort Marlene was later recycled into the FBI's main hallway.
The episode received a nomination for an Edgar Award, an honor presented by the Mystery Writers of America.
The tagline for this episode changes from "The Truth Is Out There" to "Trust No One." This phrase is spoken by Deep Throat with his dying breath.
The first season finale ends pretty much the same way as the first episode of the series: Scully waking up and the clock changing from 11:21 to 11:22 and Cigarette Smoking Man stores the alien fetus in the huge vault beneath the Pentagon as he did with the implant in "Pilot".
Mulder:...doing a Louganis out the window...
The reference is to famous Olympic diver, Greg Louganis, who was a world-class diver, but is probably best known for a disastrous dive when he hit his head on the board on the way down, the outcome of which could have been very serious indeed.
Carpenter: We've come a long way from Colonel Mustard in the Den with the Rope haven't we?
An obvious reference to the popular board game, Cluedo (or Clue as it was renamed in America), where people have to discover whodunnit, where and with what! In England the Den would have been the Study. The allusion is to the fact that we no longer have to take a best guess, but that science can pinpoint the culprit based on a number of factors, such as fingerprints, DNA etc.
Movie Reference: Raiders of the Lost Ark
The final scene, where the Cigarette Smoking Man places the box containing an important item on a storage shelf in a vast warehouse space in the Pentagon filled with nondescript boxes, is very reminiscent of the final scene of the 1981 movie. In that movie, the first to feature the Indiana Jones character, the crate containing the Ark of the Covenant is placed on a storage shelf in a vast warehouse space in an unnamed government building. In both cases, the scene makes the point that the government is covering up important scientific finds and storing them out of the reach of the public.
Location: Zeus Storage, 1616 Pandora Street
According to Greek classical religion, Pandora was the first woman. Zeus, the King of the Gods, was angered because Prometheus stole fire and gave it to mankind. Zeus ordered the Gods to create a woman as a punishment for mankind. Pandora is credited (or blamed) for opening a box and releasing a host of troubles on the world.
Mulder: The man we met yesterday kept this place like he was waiting for the people from Good Housekeeping to show up.
Good Housekeeping is a women's magazine which was founded in 1885.
Lacerio: I know it's not Silence of the Lambs, but it's what we do.
Silence of the Lambs is a novel by Thomas Harris which was successfully adapted for the big screen in 1991 by Jonathan Demme. The movie stars Jodie Foster and Anthony Hopkins and tells the story of an unexperienced FBI agent, Clarice Starling, who is sent to interview the imprisoned sociopath Hannibal Lecter in order to advance her investigation of another serial killer.
Scully: He was working on the Human Genome Project.
The Human Genome Project (HGP) was initiated in 1989 as an effort to map the human genetic code, and it continues to this day.
Mulder: Why don't we just cut out the Obi-Wan Kenobi crap.
Deep Throat acting like Obi-Wan Kenobi is taken from The Empire Strikes Back and Return of the Jedi, where Obi-Wan appears every now and then to give Luke some advice and guidance.