Homer and Bart watch a TV movie called The Krusty the Clown Story: Booze, Drugs, Guns, Lies, Blackmail and Laughter, which reveals that Krusty won four Emmys, but they keep getting interrupted by Lisa playing her saxophone in her bedroom. Homer asks her to stop and Lisa responds that she has to have an hour of practice every day. Bart enters Lisa's bedroom and tries to grab the saxophone from her, but he inadvertently tosses it out the window. It lands in the middle of the street and is run over by a car, a truck, a man riding a tricycle, and stomped on by Nelson Muntz. In a period of mourning, Lisa reveals she cannot remember ever not having that saxophone, so Homer recounts the instrument's origins.
In a flashback to 1990, Bart goes to his first day of school, but things do not go so well for him. Bart's initial enthusiasm is crushed by an uncaring and bitter teacher who says that he would be a failure at life, and he draws a violent sketch of his feelings. Marge becomes worried that something is truly wrong with him. It is during discussions of Bart's future that the school psychologist realizes the young Lisa completed a complicated puzzle of the Taj Mahal, telling Homer and Marge that they need to nurture her gifted spirit. They try to send Lisa to a private school but the tuition fee costs $6,000. Meanwhile, a terrible heat wave hits Springfield and Homer saves $200 to buy an air conditioner. Marge, however, asks Homer not to buy one until they figure out how to help Lisa. At the school, Bart talks with his future friend Milhouse and makes a farting sound, which Milhouse finds amusing. Encouraged, Bart entertains a group of children with rude words and when Principal Skinner tells him to stop, Bart replies "eat my shorts" and starts humming the Batman theme, replacing the word "Batman" with "Buttman", setting out on his path to become the school prankster.
On his way to purchase a new air conditioner, Homer discovers that a musical instrument is a way to encourage a gifted child, and subsequently sacrifices his air conditioner money to buy Lisa her first saxophone. He asks the clerk to engrave on the sax: "Dear Lisa. Never forget your daddy loves...", but finishes the sentence with a "d'oh!" as he drops the saxophone by accident. In the present, Marge mentions that there is some money in the air conditioner account. Homer complains that the house has had no air conditioner for many years, but decides to buy another saxophone for Lisa, which was inscribed, "Dear Lisa: May your new saxophone bring you years of D'oh!" Lisa then plays the saxophone hook from the song "Baker Street."