Lisa confronts Principal Skinner at school, concerned that lessons spent watching videos aren't helping her realize her full potential, but is rebuffed by Skinner telling her that if he did make it harder other students would be in his office complaining about the curriculum like she is. Meanwhile, Bart manages to link up several police megaphones together and then says "testing" into one. The word is amplified by the megaphone which is further amplified by the next and so on until a sonic shock wave is realized that's powerful enough to shatter every piece of glass in town and renders the population temporarily deaf. Homer and Marge decide to take Chief Wiggum's advice and put him in Rommelwood Military School (luring Bart into the car with the lie that they're going to Disneyland). Bart does not want to be there from the get-go, but Lisa sees the education the cadets receive and decides to stay there with him. Marge tells Lisa that if she wants to quit and come home at any time she can, but ignores Bart's pleas for just that.
Both of them get a hard time from the other cadets: Bart starts to fit in after a while, the others calling him a "natural solider," while Lisa, the first female ever to join the academy, remains an outcast despite enduring the same hazing as her brother. Bart tries to keep her spirits up, while keeping the fact that he cares about her a secret from the others.
At the end of the term, a final challenge awaits all the students; they must pass a physical test called "The Eliminator." In the Commandant's own words, it's a "150 foot hand-over-hand crawl across a 60 gauge Hemp-Jute line with a blister factor of 12. The rope is suspended a full 40 feet over a solid British acre of Old Growth Connecticut Valley Thorn Bushes." Bart helps Lisa to train in secret. The others cheer when she nearly falls off, and Bart starts calling out helpful thing such as "Come on, you can do it!" and "I believe in you, Lisa!" They both pass, and Lisa receives a medal for "Satisfactory Completion of the Second Grade."
Homer and Marge pick up Bart and Lisa from school, and agree to take them to Disneyland for real, but it turns out they've been tricked again, as they're being taken to a dentist—which makes Bart and Lisa sad, but Homer and Marge find it funny.