Having realized that Krusty has erased all the archival tapes of his show from the Sideshow Bob era, Bob schemes to hypnotize Bart to blow up Krusty live on the air.
When the popular game show Me Wantee! steals ratings from The Krusty the Clown Show, Krusty, annoyed with the network executives who refuse to stop pestering him even when on air, announces his fifth—and-final retirement. During an interview with Kent Brockman, Krusty says that he is tired of doing his show, and admits to taping Judge Judy over all his old shows featuring Sideshow Bob. Unfortunately, Bob is one of those who watches as Krusty makes his confession.
Enraged at the revelation, Bob vows revenge by plotting to kill Krusty. He is released from prison and gets a job at Springfield Elementary as an assistant janitor. However, Skinner plans to make him the morning announcer because he admires Bob's voice. During the morning announcements, Bob tells Bart to meet him in the abandoned tool shed. Bart goes into the shed out by the playground, where Bob greets him with the usual, "Hello, Bart" but Bart simply replies, "Oh, it's just you, Bob." When Bob asks him why he isn't scared, Bart says that usually Bob just gets arrested in the end. Bob then ties the helpless Bart to a chair with rope and hypnotizes him, and programs him to smash a statue of Krusty at a local Krusty Burger, getting Cletus to take his picture. Chief Wiggum sees Bart smashing up the statue but doesn't seem to mind as Bart is using a wooden bat. The next night is Krusty's farewell special, and as Krusty describes the history of his career, Bob straps Bart with plastic explosives in order to kill Krusty.
Bart is sent to hug Krusty, thereby setting off the explosives, but before he can, Krusty talks about how he regrets mistreating Sideshow Bob. Bob decides not to go through with the plan, but does not have time to stop Bart from taking to the stage. Luckily, Mr. Teeny, Krusty's trained chimp, seizes the life-threatening explosives, and throws them into the network executives' office (the executives are blown up, but reform ala T-1000).
Bart comes out of his hypnotic trance for good, and he and his family have dinner with Krusty, Bob and Sideshow Mel in a restaurant. Although Krusty and Bob reconcile, Bob is sentenced to death by guillotine; however this execution is cancelled after he tells Chief Wiggum that he should have a trial for what he did.