Because of the 2007 WGA writers' strike, the Gormagon story arc was fast-forwarded and this episode served as the closing episode for that arc. Originally, the arc was planned to last through the original order of 22 episodes.

This episode marks the final appearance of Eric Millegan (Dr. Zack Addy) as a main cast member.

Hodgins: Hey, how are you, Zack?
Zack: Quite severely injured.

Booth: There's got to be other stuff going on here, right?
Sweets: What?
Booth: Transference, uh paranoia. Come on! I mean, when I offer her a piece of pie, you say it has deeper meaning!
Brennan: I don't like pie, Booth.
Booth: Apple pie. She doesn't like baked pie.
Brennan: I don't like my fruit cooked.
Sweets: Okay, changing the subject is a way to avoid your feelings.
Booth: My feelings? Okay, now you're attacking my feelings?

Booth: Next time I die, I promise that I will tell you.
Brennan: I'll look forward to that.

Angela: I would like to welcome all of Dr. Brennan's grad students to Limbo.
Bones: It's modular skeletal storage. I don't like the moniker "Limbo."
Angela: Over 10,000 lost souls remain here, sweetie. Unidentified. Waiting. It's a good name; let's just go with it.

Brennan: It's Zack. He's the killer, Booth. It's Zack.

Brennan: All of your assumptions are built upon a first principle, Zack. To wit, the historical human experience as a whole is more important than a single person's life.
Zack: Yes.
Brennan: Yet you risked it all so you wouldn't hurt Hodgins.

Brennan: I knew I shouldn't have gone to that funeral. It was a complete waste of time just like I said.
Booth: Wait a second, you thought that my funeral was a waste of time?
Cam: I thought it was a lovely service Booth.
Booth: Thank you! You know, I expected to see more people though.
Hodgins: I always imagined a lot of ex-girlfriends crying.
Booth: Yeah, me too.
Angela: You guys are pathetic.
Brennan: (to Booth) Just know I won't be attending your next funeral.
Booth: Bones, I'm telling you, you were supposed to know that I wasn't really dead, I swear! That's why I thought you weren't crying!

(about the woman who shot Booth)
Brennan: That woman was aiming at me. I would have happily taken that bullet.

Brennan: (to Booth) Just so you know I find your lack of puritan modesty very refreshing.

Cam: A toothless cannibal just can't cut it in today's competitive serial killer climate.

Hodgins: Since when did I become the assistant?
Zach: Since I became the uncontested King of the Lab.

Angela: (to Brennan) Look, I know how you see things, and I respect that. But, I need to ask you a favor. I have to go to the funeral. I'm not going to be able to get through this alone. I've been crying for like, days. I really need your shoulder here. I need my best friend.

The clocks in Booth's bathroom are all set to different times.

While Sweets is giving his TV interview, the victim from "Death in the Saddle" is shown. However, that episode was not part of the Gormagon killings.

Earlier episodes stated Gormogon only uses widow's sons as apprentices; however, both of Zack's parents are alive.

Brennan says 180 centimeters is about 5'8". However, 180 is just shy of 5'11".

The comic book Booth is reading in the bathtub is from the "Green Lantern" series of books. David Boreanaz was the voice of the Green Lantern in the 2008 video Justice League: The New Frontier.