After a day watching mind-numbing videos in class, Lisa becomes concerned that her education is not challenging enough. Meanwhile, Bart's class visits the Springfield Police Department, where Bart is left alone with several megaphones. After placing them end to end to increase their amplification, he inadvertently creates a sonic shockwave that shatters all the glass in Springfield. Chief Wiggum suggests sending Bart to military school to correct his behavior. When the family visit the school, Lisa is impressed by the challenging curriculum and decides to attend with Bart.
Lisa stirs discontent among the students, as she is the first female student and gets her own barracks. She and Bart are subjected to hazing; Bart is eventually accepted and distances himself from his sister. Lonely, Lisa considers going home, but decides to see it through. As the school year comes to a close, the Commandant reveals the final test for the students: the "Eliminator", a hand-over-hand crawl across a rope suspended above thorn bushes. Lisa fears she will not be able to complete the task, but Bart helps her train in secret.
On the day of the test, Lisa is the last to cross the Eliminator. She is about to fall and the students jeer, but Bart cheers her on and she makes it across safely. The other students vow to make the rest of the semester a living hell for him, but realize they graduate in three hours. The Commandant awards Lisa a special medal "For Satisfactory Completion of the Second Grade".