Towards the end of the autopsy scene, Scully has her back to the wall while talking to Mulder on her phone. If you look closely, you can see the crew member's shadows moving across the wall behind her.
When the cell phone rings during the scene in the crypt, Mulder uncovers the dead body with the phone in its hand. The display on the phone says "Micah Hoffman". Why then would they assume that it was Micah Hoffman's phone since caller ID indicates who is calling, not who owns the phone.
This episode was loosely based on the real life case of Mark Hofmann who many believe is the one of the most successful forgers in history. He successfully fooled the Church of Jesus Christ of Latter-day Saints to buying counterfeit documents that cast the church in bad light.
Federman: Well. From counter culture to counterfeiter.
Mulder: Alright, one more pun and I pull out my gun.
Rational Zombie: Come on, man. Don't break the bowl. We don't want to go back to being dead. There's no food, no women, no dancing. Save the bowl and we'll dump that Ciggy-Smoking Stooge for you and you'll be the new King of the Dead.
Garry Shandling as Mulder: I'd rather serve in Heaven than rule in Hell.
Movie Director: Turkey. Miss Leoni's shoulder is made out of turkey.
Garry Shandling: Do you dress on the right or the left?
Mulder: Wh..huh..what do you...
Garry Shandling: Look, I play a character, I need to find his rudder, his center...
Mulder: I guess mostly to the left.
Garry Shandling: Mostly?
Mulder: Most of the time.
Garry Shandling: Wardrobe!
Mulder: Federman, that wasn't a movie, that was real life.
Federman: The difference being?
Scully: Mulder, we should have a warrant.
Federman: Hey, it's only the Constitution. No big deal.
Federman: You want my advice? You're both crazy.
Mulder: Why do you say that?
Federman: (to Mulder) Well, you're crazy for believing what you believe. (to Scully) And you're crazy for not believing what he believes.
Scully: Did your linguist happen to translate it?
Burks: Yes, he did. It's in two parts. The first part, here, roughly translates to "I am the walrus. I am the walrus. Paul is dead. Coo-coo-ca-choo." Although, there is no Aramaic word for "walrus", so it literally says "I am the bearded, cow-like sea beast."
Scully: Mulder, I have something to confess...
Mulder: What's that?
Scully: I'm in love with Associate Producer Walter Skinner.
Mulder is watching Plan 9 from Outer Space
Scully: How -
Scully: You've seen this movie 42 times?
Scully: Doesn't that make you sad? It makes me sad.
Skinner: Agent Scully... if I'm carrying Marilyn Monroe's purse do you assume that I slept with J.F.K.?
Federman: Just curious if she's more than your doctor.
Mulder: Enough, Wayne.
Federman: Hey, whatever.
Zombie actor: The people are made out of turkey!
Garry Shandling as Mulder: You know, seven long years I've been waiting for just the right moment, Scully.
Téa Leoni as Scully: Oh, you're a sick man, Mulder. Go on.
Garry Shandling as Mulder: I love you, Scully. No ifs, ands or...
Téa Leoni as Scully: Bees.
Scully: Do you think it's at all possible that Hoffman is really Jesus Christ?
Mulder: Are you making fun of me?
Mulder: Well, no, I don't. But crazy people can be very persuasive.
Scully: Well, yes, I know that. Maybe true faith is really a form of insanity.
Mulder: Are you directing that at me?
Scully: No. I'm directing it at myself and at Ed Wood.
Cigarette Smoking Pontiff: I'll offer you a deal. You give me the Lazarus bowl and I'll give you Scully.
Téa Leoni as Scully: Mulder!
Garry Shandling as Mulder: How about this deal? You give me Scully, I don't smash the Lazarus bowl and shove the pieces where the Son of God don't shine you Cigarette-Smoking Mackerel Snapper.
Scully: It's all over now.
Mulder: No, no, it's just beginning. Hoffman and O'Fallon were these complicated, flawed, beautiful people and now they'll just be remembered as jokes because of this movie. The character based on O'Fallon is listed in the credits as "Cigarette-Smoking Pontiff". How silly is that?
Scully: Pretty silly.
Mulder: Yeah, what about us? How are we going to be remembered now 'cause of this movie?
Scully: Well, hopefully, the movie will tank.
Mulder: What about all the dead people who are forever silent and can't tell their stories any more? They're all going to have to rely on Hollywood to show the future how we lived and it'll all become... oversimplified and trivialised and Cigarette-Smoking Pontificised and become as plastic and meaningless as this stupid plastic Lazarus Bowl.
Scully: I think the dead are beyond caring what people think about them. Hopefully we can adopt the same attitude. You do know that there aren't real dead people out there, right? That this is a movie set?
Mulder: The dead are everywhere, Scully.
Mulder: (on phone) Hey Scully, Skinman's calling from a bubblebath.
Skinner: It's still me, Mulder!
Mulder: Uh... So what are you up to right now, sir?
Skinner: I'm taking a bubble bath.
Téa Leoni as Scully: Wait, wait, Mulder... I can't.
Garry Shandling as Mulder: I know this feels wrong because we're friends and we treat each other as equals, but-
Téa Leoni as Scully: No, no, it's not that. It's not that.
Garry Shandling as Mulder: Well, what then?
Téa Leoni as Scully: I'm in love with Assistant Director Walter Skinner.
Mulder: That's it, Scully, I can't take it any more.
Scully: Shh, Mulder, sit down.
Garry Shandling as Mulder: What does he have that I don't have?
Téa Leoni as Scully: A bigger flashlight.
Mulder: (to Skinner) Sir, have I pissed you off in a way that's more than normal?
While taking the bubblebaths, Scully tells Mulder that she thinks that both Téa Leoni and Gary Shandling have a crush on Mulder. Both are in-jokes: the first to the fact that Leoni and Duchovny are married; and the second to the fact that on the Larry Sanders Show, Larry Sanders, played by Garry Shandling, thought that David Duchovny had a crush on him.
Although not proven to be true, Jodie Foster's name came up when describing Scully's character portrayal. Jodie Foster was one of the choices to play Scully but Foster's contract banned her from playing an FBI agent in anything other than The Silence of the Lambs.
She went on to voice the tattoo Betty in the Season 4 Episode 13; 'Never Again.'
Not only was Scully modelled on Jodie Foster's character in The Silence of the Lambs; moreover, when Foster refused to continue the role in the sequel Hannibal, Gillian Anderson was offered the part (which was finally played by Julianne Moore).
Mulder suggests Richard Gere to play him in Federman's movie, an in-joke as David Duchovny was often compared to Gere during the early years of his career.
If you look very closely you'll see that in the scene in which the characters which are "loosely" based on Mulder and Scully roll down the hill it's actually David Duchovny and not Gary Shandling who's rolling downhill with Téa Leoni.
Scully is described as "Jodie Foster's foster child on a Payless budget" - referencing the fact that Agent Scully was indeed originally modeled on Foster's character from Silence of the Lambs.
Mulder is described as a "Jehovah's Witness meets Harrison Ford's Witness" - Harrison Ford's Witness is the answer David Duchovny got wrong on "Who Wants to be A Millionaire".
David Duchovny and Téa Leoni were married on 6th May 1997 and Téa gave birth to their daughter Madelaine West on 24th April 1999.
If you look closely as the camera pans over the audience in the theater, you can see Chris Carter, actors Minnie Driver and David Allen Grier and several crew members watching the movie. Both Driver and Grier starred with Duchovny in the movie "Return To Me" which was released a few weeks before this episode aired, which probably accounts for them being on the show.
Movie Connection: Plan 9 from Outer Space.
Mulder is watching this movie and quoting the lines from it as Scully walks in. The plot of Plan 9 being about aliens raising human corpses to become their slaves, the theme of resurrection runs throughout this episode.
Biblical Connection: I am who I am.
This is one of the usual translations of the supposedly true name of God - YHWH.
Mulder: Twisted sister my type of nun, ya know.
This is a reference to the Heavy Metal band Twisted Sister which was popular from 1972-1988 then 1997 - present.
Garry Shandling asks Mulder whether he dresses on the left or the right. This refers to tailored men's pants having a little extra room in the top right or left inseam to accommodate male anatomy. This is why he calls "Wardrobe!" after asking about this.
Wayne Federman: You don't need a weatherman to know which way the wind blows.
This is a quote from the Bob Dylan song "Subterranean Homesick Blues."
Chuck Burks: The first part here roughly translates as "I am the walrus. I am the walrus. Paul is dead. Coo-coo-ca-choo."
This is a reference to a song called "I am the Walrus" by The Beatles. Paul McCartney is one of the Beatles.
Wayne Federman: How about the Shroud of Turin?
The Shroud of Turin is an ancient linen cloth bearing the image of a man who appears to be crucified. Many worshippers believe it could be the cloth that covered Jesus Christ when he was placed in the tomb.
Wayne Federman: It's a Silence of the Lambs meets Greatest Story Ever Told type thing.
Two films. Silence of the Lambs is a thriller about the cannibal Hannibal Lecter who aids an FBI agent (Jodie Foster, who was already mentioned earlier in the episode) in the search for a murderer. For the sequel to this movie, Hannibal, Jodi Foster declined to return as the Clarisse Starling. Gillian Anderson was briefly considered to replace her, but her contract with X-Files did not allow her to take a role as another FBI agent.
Greatest Story Ever Told is a drama about the life of Jesus Christ.
Scully: you've seen this movie 42 times?
The number 42 is the answer to life, the universe, and everything, according to popular science fiction series, The Hitchhiker's Guide to the Galaxy written by Douglas Adams.
Mulder's comment has also been featured for over twenty years as a tag line for Art Kumbalek, a fictional columnist or Milwaukee (WI US) newspaper Shepherd Express. Each week, Art For Art's Sake opens with, "I'm Art Kumbalek and man oh man manischewitz what a world, ain'a?"
Name: Micah Hoffman
Micah Hoffman was named for Mark Hoffman. In the 1980's, Mark Hoffman made extremely good forgeries that seemed to cast doubt on the origin of the Church of Jesus Christ of Latter-Day Saints (Mormons). The most prominent of these was the 'Salamander Letter' that received national coverage. The forgeries passed several tests and were at one point declared authentic, but Hoffman's Mormon accomplices were threatening to expose him as a fraud. Hoffman planned to kill them by blowing them up with home made bombs. When one of his own bombs went off early and hurt him, it started an investigation that exposed most of what he had sold over many years as fake, including the Salamander Letter, rare coins, other documents etc.