- Alternative Character Interpretation: Some people believe that after Stewie killed Denise Crosby to show them he wasn't screwing around, the rest of the Star Trek cast decided to act as annoying and unbearable as possible on purpose so Stewie would send them home sooner. If so, this was a pretty big Batman Gambit on their part, since Stewie could essentially kill them whenever he wanted.
- Anvilicious: Although it has plenty of fans, this episode is unfortunately loathed by many for essentially stating that the religious (especially Christians) are all book burners who hate athiests, and that God does not exist because of Meg's Butt Monkey status.
- Critical Dissonance: While most critics most thought it was So Okay, It's Average (they hated the main story because it focused on Meg, but loved the Star Trek story and some of the jokes), it's considered by other fans to be one of the worst episode of the show, whilst by some fans to be a good episode.
- Family-Unfriendly Aesop: This episode basically tells people that it is wrong for them to practice religion.
- Harsher in Hindsight: The scene of Brian's Prius being thrown through the house is a little more disturbing given the news of Toyotas being recalled for faulty brakes (for those who don't know, Prius is part of the Toyota brand).
- Ho Yay:
Brian: Are you queer?Stewie: Probably.
- Jerkass Woobie: Brian, since his treatment initially was a tad unfair.
- Memetic Mutation: "Hwil Hweaton."
- The Woobie: Meg.