In this episode, we see the fourth and final kiss between Mulder and Scully. While it is true that this is the fourth episode in which Mulder and Scully kiss, they share multiples kisses in this episode.
In this episode, we finally know for sure that Mulder is the father of William. When the guards are questioning him, he says he's thinking about his son and his mother.
Scully's full name is Dana Katherine Scully.
Mulder's full name is Fox William Mulder.
Scully: Mulder, it's not funny when you pull that stupid act.
Mulder: No, it is funny. What's not funny is what they do to you if you don't pull that stupid act. (He kisses her, and she kisses back)
Scully: (Crying) Our son, Mulder. I gave him up... I gave him up.
Mulder: (Crying) I know you had to... I just miss you both so much...
Prison Guard: What are you thinking?
Mulder: About my son... About his mother.
Kallenbrunner: Well, what I mean is, you have no proof to back up one word you just told us. (Scully is silent) Agent Scully, isn't it true that you and Mulder were lovers, and you got pregnant and had his love child?
Kallenbrunner: Thank you. Next witness.
Scully: Guilty on a lesser charge. Maybe they'll go for it, let you walk out of here.
Mulder: I'd rather die, Scully. I'd rather die than give them what they want.
Scully: How can you say that -to me?
Mulder: This is greater than you or me. This is about everything we've worked for, for nine years. The truth we've both sacrificed so much to uncover.
Mulder: Come here you big, bald, beautiful man.
Skinner: The only thing you're going to be kissing, Mulder, is your sweet ass good-bye.
Mulder: It's not about how good you are, they control the game...they own it.
Doggett: Then lets shove it up their ass.
Mulder: If I am a guilty man, my crime is in daring to believe; that the truth will come out and that no one lie can live forever. I believe it still. Much as you try to bury it, the truth is out there. Greater than your lies - the truth wants to be known.
Mulder: You may have rid yourself of your headache, but you've only done it by cutting off your own head.
Mulder: I smelled you coming, Clarice.
Reyes: What are you trying to do, destroy a man who seeks the truth, or destroy the truth so no man can seek it? Either way you lose.
Mulder: I just missed all of you so much.
Mulder: Maybe there's hope.
In the final scene of the episode, the X-Files Theme is heard in the background slowly "whistled" in a major key, instead of the ubiquitous minor key of the series' opening/closing credits
The time when Knowle Rohrer (who Mulder was convicted of killing) pulls up to the USMC Base Brig to 'retrieve' Agent Mulder is 11:21 pm. Chris Carter's wife was born on 11/21.
Director Kim Manners provides DVD commentary on the complete season 9 DVD set.
Even though they died in "Jump the Shark" The Lone Gunman's ghosts talk to Mulder for a short time.
The final scene is a bookend to a scene that was in the Pilot, where we first learn of Mulder's sister's abduction.
David Duchovny (Mulder), Gillian Anderson (Scully) and William B. Davis (Cigarette Smoking Man) are the only actors to appear in both the first and last episodes of the series.
A cut scene as revealed by the Season 9 DVD collection shows a different ending: President Bush being notified of Mulder's actions and saying "The American people already know the truth, they just don't believe it!" The scene was ultimately cut by Chris Carter and Frank Spotnitz because it ruined the tone of the previous scene (Mulder and Scully holding each other)
December 22, 2012 is the day the ancient Mayans predicted that the world will end.
The Mayan calendar ends on December 21st, 2012, but it has never been determined that this is because they predicted the end of the world on this date.
David Duchovny's name returns to the opening titles in this episode.
Fox Mulder: I smelled you coming, Clarice.
This is a reference to the movie Silence Of The Lambs (1991).