When Lisa protests against genetically-modified foods, she discovers that the town's newest chemical engineering plant is owned by none other than Sideshow Bob, who's using the plant and the position to genetically modify himself. Meanwhile, Marge becomes a church volunteer to help horny teenagers become abstinent.
- Apathetic Teacher: Ms. Hoover's approach to teaching the solar system is so half-assed, she does nothing but show an outdated documentary on Nepture. Apparently, she declined to use Lisa's more competent lesson plan.
- Antagonist in Mourning: Nelson admits to Flanders he misses Mrs. Krabappel.
- Bait-and-Switch: After Bob kicks his prison cement block through a ceiling window, the scene shows Hans Moleman advertising a kiosk of porcelain figurines. Hans promptly gets crushed by the block.
- Berserk Button: After warning Bart and Lisa that he's injected himself with DNA from zombie ant fungus and "could be tipped into a murderous rage by the slightest provocation", Bob is accosted by a woman who asks him to take a cellphone picture of her with her family... and another for safety... and then another, because "I think my eyes were shut in that one"... and yet another, "with my husband's camera" until Bob finally snaps.Bob: THEY'RE ALL UGLY 'CAUSE YOU'RE IN THEM!
- Continuity Nod: One featuring Bob's face, and another to Springfield Dam.
- The Dragon: Lisa, briefly, becomes Sideshow Bob's.
- Diabolus ex Machina: Sideshow Bob can't escape his old nemesis the rake, even underwater.
- Driven to Suicide: When Sideshow Bob realizes what he has become, he attempts to drown himself, forgetting that he gave himself gills among his genetic alterations.
- Heh Heh, You Said "X":Bart: The jig is up, Bob! Return the spear to the Homo erectus! [sniggers] Homo erectus! Where has that word been all my life?!
- High-HeelFace Turn: Lisa, after spending most of the episode as Sideshow Bob's Dragon.
- Nausea Fuel: The teens Marge is trying to pitch abstinence to consider her sleeping with Homer to be this In-Universe.
- Non Sequitur: The last scene is a random Imagine Spot by Flanders of him dancing with Edna Krabappel, commenting on how he misses her and Nelson showing at the window saying he misses her too. The episode hadn't featured either character until this last bit. This was a form of In Memoriam, Marcia Wallace had died some months previously (the Chalkboard Gag for "Four Regrettings and a Funeral" simply said 'We'll miss you, Mrs. K') and this was the last episode Edna appeared and Wallace's last performance for the character, so they gave her an energetic dance scene wearing a stunning red dress.
- Not That Kind of Doctor: When the family discover who the plant's Chief Scientist is.Simpsons: AAAAGH! SIDESHOW BOB!
Bob: Doctor Sideshow Bob.
Homer: Real doctor or Ph.D.?
Bob: (sourly) Ph.D.
- Play-Along Prisoner: Thanks to his genetic modifications, Sideshow Bob can break himself free from the prison's chain and block anytime he wants and he can kick the block away like it's a regular ball.
- Shout-Out: To "Titanic" when Willie sacrifices himself to save his Companion Cube.
- Sinister Minister: Reverend Brogan, Lovejoys predecessor who was arrested in the past, which led to finger puppets being removed from the Church
- Would Hurt a Child: Sideshow Bob chases the Simpson kids throughout Springfield and nearly throws them off the Springfield dam once he catches them. Bob's actions aren't really surprising, as Lisa had to get Bob to promise to not hurt Bart before she was even allowed to accompany him.