Doggett mentions that there were three rounds missing from the clip of Mulder's Walther PPK. This is inaccurate as the Walther uses a magazine and not a clip. Furthermore, an FBI Agent and former U.S. Marine would understand this distinction and not make such a blunder.
Doggett: A.D. Skinner, you're here late.
Skinner: So are you.
Doggett: I wanted to finish my case report before Agent Scully comes in tomorrow morning.
Skinner: Have you?
Doggett: I don't even know where to begin or how to explain it. Only thing I do know is is I'm no closer to finding Mulder now than when I started this thing.
Skinner: You got inside of his head, Agent Doggett. You understood why Mulder did something I wouldn't have thought him capable of doing. You want some free advice? Don't write that report. You turn that in you open up a world of trouble for Agent Scully. And yourself.
Doggett: She didn't know anything about this, sir. Of that I'm certain.
Skinner: How many months will be lost proving that? How much damage done to her good name? And Mulder's? And to yours? For what?
Doggett: The truth.
Skinner: You and I both know what happened out there, Agent Doggett. No one else needs to.
Byers: We learned what we could. This is somewhat short notice, of course.
Frohike: And a little outside our area of expertise.
Langly: Plus the fact we were sleeping.
Doggett: You wearing pants, Langly?
Skinner: You want the truth? Then ask Agent Scully!
Doggett: I can't do that.
Skinner: Why not?
Doggett: Because she... she signed those case reports, too.
Skinner: You take that story to OPR, the accusation alone could cost Scully her job.
Doggett: I'm not taking it to OPR. I'm taking it to you.
Doggett: This is the muzzle of Mulder's pistol. You see that there?
Skinner: It's blowback.
Doggett: Macrospatter of dried blood in a semi-circular pattern. Which indicates Mulder fired close-range at something or someone.
Skinner: I've heard enough.
Doggett: Where are you going?
Skinner: It's where you're going, Agent Doggett. You're trying to build a case that what? Mulder killed a man and then made himself disappear? That's not what happened. I told you before, he was abducted. I saw it!
Doggett: Agent Mulder signed falsified case reports.
Skinner: Oh, come on, John, this isn't about Mulder, it's about you! Your career. You give the FBI a narrative for Mulder's disappearance, you're off the X-Files and back on the fast-track to the directorship.
Doggett: I'm just trying to find the truth.
Sheriff Frey: Like I said, Agent Doggett, I hate to waste your Saturday.
Doggett: The Hangemuhls own a gun, Kurt?
Sheriff Frey: No, I don't think so. Why?
Doggett: I saw three holes plastered over in their living room wall.
Sheriff Frey: Gunshots?
Sheriff Frey: You want to go back and ask 'em?
Rustic Woman: (to Doggett) All these years, we didn't know what it could do. It took your death. You freed it.
Mulder is mentioned as having a Walther PPK as a second weapon - the same gun he used to kill John Lee Roche in "Paper Hearts".
Mulder and Scully both briefly return in this episode, albeit in flashbacks.
Byers: Agent Dogbert...
In the teleconference between Doggett, Skinner, and the Lone Gunmen, Byers refers to Doggett as "Agent Dogbert." This is a reference to a character in the comic strip Dilbert written by Scott Adams.