When looking for the spare car key in the key drawer (to get to Maggie, who locked herself in the car along with the car keys), the Simpsons find keys that lead them in three directions; Homer has the key to the Duff Brewery, which leads to a joyride in the Duff Blimp; Marge and Maggie find a key to a wind-up train that makes flatulent noises; Lisa finds a key to a room of "Banned Band Books" which is really a mysterious empty classroom.
After visiting and purchasing from a vendor that sells cakes from cancelled weddings, Maggie accidentally gets locked in Homer's car with the keys inside. While searching for the spare keys, which soon proves unnecessary, as Maggie freed herself, the Simpsons discover a collection of keys to every door in Springfield. Homer also explains some of the keys history to the kids, which included keys to various jobs he had, as well as one key that he and Marge attempted to bring to a key party before realizing what a key party was (and were implied to have attempted to leave as soon as they found out).
Deciding to return one of the keys to the school, Lisa comes across a hidden classroom filled with props underneath the school, behind the sign that says, "Banned Band Books". She is very intrigued about the discovery, so she shares it with Principal Skinner. When they go down with Martin, Database and a few other students, Lisa opens the door and what is behind the door is simply a bookshelf full of banned band books. Later, it becomes apparent that Skinner and Superintendent Chalmers are hiding something, as they snatched the key from her. However, Lisa has it replicated and returns to the door. She touches the bookshelf and it simply falls apart. She goes into the classroom and a mysterious cloaked figure is writing, "The children are on Bus 23." Lisa screams, prompting the figure to run away.
After sorting out all the keys, Marge and Maggie find a key for a wind-up toy train called "The Pooter Toot Express", which Marge figures must be her anniversary present, which makes farting noises when it moves. The toy gets away from them and they must chase it throughout the city.
Meanwhile, Bart tries causing mayhem with the keys but all what is produced is good deeds, such as when he uses the window washer to moon everybody in the high-rise. Gil tries to commit suicide, and when he hits the window washer, he calls Bart a "naked fairy god-boy," and Bart receives a key to the city from Mayor Quimby.
Meanwhile, Homer finds a key to the Duff Brewery (it's implied that he got it from Duffman who proceeded to commit suicide by drowning from skinny-dipping in regards to being denied a drink), and he and Barney adventure in it. Homer flies off in the Duff blimp, but he drinks AND texts while flying it.
With help from Bart, Lisa asks Nelson, who has been held back at Springfield Elementary more times than he can count, about Bus 23. Nelson explains that some years ago, he saw a bus loaded with kids, whom he planned on extorting for money. However, he spotted Skinner and Chalmers arguing on which route the bus should take. Chalmers insisted on it hurrying past the ice bridge. After that, "The bus never came back." Lisa and Bart want to find Bus 23, so they make Homer fly them there on the Duff Blimp. Lisa falls out into the water, and discovers that all the children are mannequins. Otto, who was the cloaked figure, feels safe at last because now he knows he didn't kill twenty-four children.
Chalmers and Skinner try to flee to Bolivia, only for Bart to snag Skinner's car keys; Skinner was slow on the uptake that Bart had his keys. They are forced to explain that years ago, they had gotten a cheque from the government for the school improvements. However, Skinner cashed the cheque and stuffed the money in his pants, which were put in the laundry by his mother without his knowledge, destroying the money. To prevent the government from finding out, Skinner, Chalmers and Groundskeeper Willie had to fake the classroom with the mannequins and photograph everything. But because they could only afford to rent the mannequins, they had Otto drive across the ice bridge before they had to pay for the extra day. Chalmers and Skinner then apologize to Otto for making him think that he was responsible for the deaths of 24 children. Lisa pointed out that they didn't count on two things: Homer buying a wedding cake and Maggie getting locked in the car. Skinner admits that he saw the cake coming but not Maggie. Chalmers berates him for that.
In the epilogue, Otto is horribly driving the bus on an icy bridge and he says, "Not to worry. They're just mannequins." Then Milhouse tells him otherwise, trying to prevent Otto from driving off the bridge. The icy surface causes the bus to careen close to the edge. Otto thinks that they will fall slowly like in Inception, only for his ride to plunge into the river below.