In this episode, Scully says that she and Mulder have known each other for four years. This is incorrect, because their first case together took place in 1992.(even though the show premiered in 1993).
Are we really supposed to believe that the DOD's only form of security is a metal detector, a bag x-ray machine, a flimsy CARD that offers access to anyone who comes across it? You would think the Pentagon would have something more high-tech (and more fool-proof), like retina scanning.
In Mulder's voiceover he says that his sister went missing 23 years ago. At least 4 years ago, in season 1's 'Conduit', Scully says that she disappeared 21 years ago. The statement here should be the correct one (Nov 1973 - early 1997) making the earlier statement the goof.
Michael Kritschgau: Hey! How'd you get in here? (Defence Advanced Research Projects Agency)
Mulder: Through the front door.
Michael Kritschgau: You can't bypass security.
Mulder: You can when you have the card. (He holds up Scott Ostelhoff's security card)
Scully: Mulder? What are you doing? Why are you sitting in my bedroom in the dark?
Mulder: It was too crowded in my apartment, I couldn't sleep.
Scully: I'm not kidding, Mulder.
Mulder: Good, 'cause neither am I. There's a dead man on the floor of my apartment and it's only a matter of time before he starts to stink the place up.
Scully: If science leads me to these ends, it is not lost on me that the tool with which I've come to depend on absolutely cannot save or protect me, but only bring into focus the darkness that lies ahead.
Mulder: In four years I have shared my partner's passionate search for the truth and if my part has been a deception, I have never seen her integrity waver or her honor compromised. But now I ask her to lie to the people lying to us -- a dangerous lie to find the truth -- to find the men who would be revealed at its enemy, as our enemy, as the enemy within.
CSM: You've been watching Mulder. You had a man on him. No one bothered to inform me of this.
Elder: I know nothing of this man.
CSM: I will not be cut out like this. You need my expertise. Is this being run from the DOD?
Elder: If it is, I am unaware of it.
CSM: I've always kept Mulder in check. I put this whole thing together. I created Mulder.
Elder: Agent Mulder is dead. Our FBI source confirmed it this morning. Mulder killed himself. Mulder was an asset. Without his partner, you may have underestimated his fragility.
CSM: I've never underestimated Mulder. I still don't.
Scully: Mulder, how long has this been going on?
Mulder: Maybe since the beginning, since you joined me on the X-Files.
Scully: That would mean that for 4 years we've been nothing more than pawns in a game, that it was a lie from the beginning. Mulder, these men... You give them your faith and you're supposed to trust them with your life.
Mulder: There are those who can be trusted. What I need to know is who among them is not. I will not allow this treason to prosper, not if they've done this to you.
Scully: Mulder, we can't go to the Bureau making these accusations.
Mulder: No, but as they lie to us, we can lie to them. A lie to find the truth.
For the first time in the series a brief synopsis of previous events is given at the very beginning of the episode, as in "Previously, on the X-Files..."
The card Mulder finds in the file cabinet lists Scully's birthdate as 2/23/64.
The X-Files upgrades to Widescreen from this Season.
The premiere also features an altered tagline, this one being 'All Lies Lead To The Truth', symbolic of Mulder's journey of following the path of lies to find Scully's cure.
The vault that Mulder accesses at the DOD is the same seen in the Pilot and Finale of season 1, where Cigarette Smoking Man stores the implant and the alien foetus.
Mulder: If this treason should prosper.
Mulder says this line in a voiceover narration in the opening scenes from the episode. It is a paraphrase based on the following verse: "Treason doth never prosper: what's the reason? / Why if it prosper, none dare call it treason." It is usually attributed to the Roman poet Ovid. Credit has also been given to English epigrammist Sir John Harrington. The point of the verse, of course, is that if treason succeeds, it becomes law. Mulder fears that if the people he opposes win, their lies will be accepted as fact.
Film References: JFK
When Kritschgau is describing the government conspiracy to Mulder it is much like a scene in Oliver Stone's JFK between Detective Jim Garrison and his informant "X", played by Kevin Costner and Donald Sutherland respectively. The scenes are very similar, right down to the use of stock footage, driving background music, and rapid, matter-of-fact line delivery.
JFK also had a "secret meeting" that took place at a race track (much like the meeting between CSM and The Elder).
Also, in Mulder's early voiceover he says "Let the truth be known though the heavens fall", which is quite similar to Garrison's line in JFK, "Justice be done though the heavens fall".