At school, after Mrs. Krabappel shows a video from 1956 to her students about the future, she tells her students to turn in their homework project (which they had three months to do). Bart did not even attempt to complete his homework, so he tries to make his homework on the fly out of odds and ends found in his desk. Unfortunately, Mrs. Krabappel does not approve, and prepares to send a letter to his parents. She gives it to Martin to mail and he heads out the door. Bart shoots an eraser at the pull station, breaking the glass, pressing the button and activating the alarm. Everyone evacuates, but Bart runs through some 6th graders and gets through them. He almost gets the letter when it drops out of the mail slot, but Groundskeeper Willie heads off with the mailbag.
Homer and Marge then receive the letter from the teacher informing them Bart is one month behind on his homework. When Homer is informed that he does not have to help Bart with this work; he is eager to increase his son's workload (commenting he wants him to "be Korean by the time he's (Bart) done"). Marge, however, is concerned that the heavy workload will dissuade Bart from liking school (ignoring or unaware of the fact that he already hates it). When Bart realizes his parents do not agree on this issue, he uses their opposing views to avoid homework entirely. Lisa explains that this is a wedge issue, an issue that sharply divides two parties.
Marge and Homer begin to argue more and more, with Bart inciting the two to argue about very minor things that even do not involve his homework, and Lisa calling him a sociopath. Marge seeks counsel from Ned Flanders, who recalls having a minor argument with Maude on the day she died. He mentions that this argument still haunts him. Marge also counsels Patty and Selma, who, eager to break up Marge and Homer, encourage her to "stick to her guns", saying that then she will be "free and happy" like them; however, knowing how her sisters feel about Homer, and then thinking about how her life could end up like theirs, Marge immediately heads out to make things right with her husband. Meanwhile, Homer falls asleep at work, dreams about accidentally killing Marge and realizes that he too wants to apologize. The two spot each other in traffic, rush out of their vehicles and embrace. They then decide to let Bart fend for himself, especially since he was the reason they got married in the first place, leaving Bart stunned when they pay no attention to any of his antics.
Bart and Milhouse then decide to play a prank on Principal Skinner. To evade capture, the two hide in the abandoned Springfield subway system where they discover the subway trains still work. They race down the tracks and cause a seismic tremor to shake the town. When Homer and Marge fail to react to this, Bart confesses to Nelson he no longer feels a thrill when he plays a prank. Nelson suggests Bart receives no gratification from pranks unless someone loses their temper.
Bart then decides to destroy Springfield Elementary, which was damaged by the first subway tremor, by driving the train under it. Homer and Marge find a note from Lisa informing them of this prank, and they decide to take immediate action. They rush to the subway station, where Homer tries to push the emergency kill switch. It is stuck, but Homer then imagines that the switch is Bart, pretends to be strangling him, and he succeeds in stopping the subway. However, the school is destroyed anyway when a flagpole falls against the already damaged building (much to Nelson and Krabappel's delight). And finally, after 21 seasons of being sent to his room, or punished in other different ways, Bart gets grounded, and for the first time ever, stays grounded, also having to tweet Homer about his current activities (despite Homer not knowing anything about Twitter, and not wanting to), and his parents have returned to their basic purpose: keeping their son in line. Lisa confronts Bart, who is bored, unhappy and suffering, due to his punishment and backlog of homework, and says that she did not write the note to Homer and Marge, noting that it is poorly spelled. She figures out that Bart himself wrote it, since he still writes "Springfield Elementery" on all of his tests, and knowing he is the only one who would misspell the name of the school he goes to every day. Bart is relieved when she tells him she will keep his secret so that everyone still thinks of him as a bad boy.