This episode changes its regular tagline "The truth is out there" for "Deny Everything". This is what X tells Mulder about the politics of the Syndicate. This episode forms part of the mytharc episodes.
The Skyland tram is most likely the Grouse Mountain tram near Vancouver in real life. You can see the Vancouver area when Mulder escapes from the tram.
Continuity: Margaret Scully tells Mulder that she gave her daughter the cross necklace for her 15th birthday. This is contradicted in season 5's "Christmas Carol."
Continuity: When Mulder is in the tram car ascending the Mountain, he pulls all of the things out from under the top left-hand seat. However, when the scene moves to Krycek in the booth, you don't see any of the things that Mulder threw out.
Plot Holes: Another example of the way "X-Files" plays fast and loose with time: Duane Barry kidnaps Scully in the evening - presumably he doesn't take her back to his home since that's the first place the FBI would look, so it's logical to assume that he immediately set off for Skyland Mountain with her. He shoots the state trooper sometime early the next day near the Blue Ridge Parkway, but although Mulder and Krycek don't figure out his destination and get on the road until sometime that afternoon, Barry somehow manages to reach the bottom of Skyland Mountain only forty-five minutes before the FBI agents do, even though he appears to have had at least a twelve-hour head start! Did he stop to do a lot of sightseeing along the way?
Continuity: Krycek and Mulder leave FBI Headquarters, to go to Skyland Mountain, in a blue Sedan. However in the next scene - as Mulder is driving and almost falls asleep - the color of the Sedan has changed to maroon.
Duane Barry: (yelling at the sky) They can't touch Duane Barry anymore!
Cigarette-Smoking Man: We tell you only what you need to know.
Krycek: I think I have a right to know.
Cigarette-Smoking Man: You have no rights, only orders to be carried out.
Mulder: I found this. (He shows a cross) It's something I... I never considered about her. If she was... if she was such a skeptic, why did she wear that?
Margaret Scully: I gave it to her on her fifteenth birthday.
Mulder: Don't you want to keep it?
Margaret Scully: When you find her, you give it to her.
Margaret Scully: I had that dream again last night. About Dana being taken away? I can't tell you how it scares me.
Mulder: It's probably scarier when you stop having the dream. Don't you think?
Mulder: Who are these people who can just murder with impunity and we can't do anything about it?
Skinner: Let it go, Agent Mulder.
Mulder: Like hell.
Skinner: There's nothing you can do.
Mulder: What can you do about it?
Skinner: There's only one thing I can do, Agent Mulder. As of right now, I'm reopening the X-Files. That's what they fear the most.
Mulder: I found this in Agent Krycek's car. He doesn't smoke. Agent Krycek was the last person with Duane Barry before he died. He was also the last person to see the tram operator before he disappeared. When I got to the top of Skyland Mountain, I saw an unmarked helicopter working the area. I believe that Agent Krycek gave away the whereabouts of Duane Barry and Agent Scully to whoever he's working with.
Skinner: And who is that?
Mulder: I don't know, the military? Some covert organization within the government? Whoever it is that man who smokes those cigarettes works for.
Mulder: Because Agent Scully got too close to whatever it is they're trying to deny. Because she had hard and damning evidence, that metallic implant in her possession. Or because her termination would prevent further involvement with me and my work.
Skinner: This is a serious allegation, Agent Mulder.
Mulder: So long as it's true.
Skinner: "Agent Krycek was hired or suborned by an outside agency to impede a federal investigation and may be responsible for the death of a suspect in a capital murder case."?
Mulder: It goes on.
Skinner: "And the possible murder of the tram operator at Skyland Mountain." There's a lot of blood on this document, Agent Mulder. Are you standing behind this, going on the record?
Mulder: Yes, sir.
Skinner: Then you damn well better have the facts to back it up.
X: This reaches beyond any of us, Mister Mulder. Even my predecessor.
Mulder: I want an answer!
X: Why kill Duane Barry if there was nothing to hide?
Mulder: You mean the government?
X: There are no answers for you, Mister Mulder. They only have one policy... Deny everything.
X: You've wasted a trip, Mister Mulder. There's nothing the Senator can do for you now.
X: Not without committing political suicide.
Mulder: Why? Do they have something on him?
X: They have something on everyone, Mister Mulder. The question is when they'll use it.
Mulder: Is Agent Krycek asserting that I killed him too?
Skinner: No. He corroborates your story. But the fact is, we've got a dead suspect, Agent Mulder, and no other plausible cause of death. O.P.C. wants the both of you to take a lie detector test. You're to report there immediately.
Mulder: There is another plausible cause of death.
Skinner: Which is?
Mulder: Poisoning by injection or ingestion.
Mulder: You won't find that on the navy pathologist's report.
Skinner: What are you saying, Agent Mulder?
Mulder: That the autopsy is incomplete. That the military covered up the toxicological findings.
Skinner: And why would they do that?
Mulder: Because they know where Scully is.
Krycek: Yeah. You really think he tracked her down with that implant?
Mulder: Well, that's the easiest explanation. It's also the most implausible.
Krycek: Is there another possibility?
Mulder: Somebody could have given him her address. I don't know who.
Krycek: You know, Chernobyl, Exxon Valdez, Three Mile Island... they were all linked to sleep deprivation. The U.S. Department of Transportation estimates that over 190,000 fatal car crashes every year are linked to sleepiness.
Mulder: Did they estimate how many people are put to sleep listening to their statistics?
Mulder: (About Duane Barry) Did you ask him about Scully?
Mulder: What did he say?
Krycek: He started whistling 'Stairway to Heaven.'
Agent: Why are you so paranoid, Mulder?
Mulder: Oh, I don't know. Maybe it's because I find it hard to trust anybody.
Krycek: If Mulder is such a threat, why not eliminate him?
CSM: That's not our policy.
Krycek: It's not? After what you had me do?
CSM: Kill Mulder and you risk turning one man's religion into a crusade.
David Duchovny performed his own stunts in the aerial tram sequence.
This episode's tagline changes to 'Deny Everything', spoken by X: "They only have one policy Mister Mulder... Deny everything".
The song that Duane Barry is listening to on his way to Skyland Mountain is "Red Right Hand" by Nick Cave and the Bad Seeds, featured on The X-Files album "Songs in the Key of X".
Krycek: He started whistling "Stairway to Heaven."
Stairway to Heaven was an influential song by Led Zeppelin.
Krycek: You know, Chernobyl, Exxon Valdez, Three Mile Island...they were all linked to sleep deprivation.
Chernobyl is the site of a nuclear power plant that exploded in 1986.
Exxon Valdez is the name of an oil tanker which caused a massive oil spill in 1989 after hitting Prince William Sound's Bligh Reef before the coast of Alaska. Three Mile Island is the location of a nuclear power plant which suffered a partial core meltdown in 1979.
Skinner: That he's following orders from alien voices in his head. Well, that's an interesting spin on the Nuremberg defense.
Skinner is referring to the Nuremberg Trials which were held in the German city of Nuremberg from 1945 to 1949. The trials were conceived to bring the major war criminals/leaders of Nazi Germany to justice. In their defense most of the accused stated that they were just following orders.
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