The Simpsons attend a play at the theater district in downtown Springfield. It’s called “Stab-a-Lot: The Itchy and Scratchy Musical,” and features Bart and Lisa’s favorite characters in an elaborate, Julie Taymor-like musical laced with the violence and mayhem associated with the cartoons. When the performance ends, audience members spring to their feet. The director, Juliana Krellner, is met with thunderous applause. Krellner tells the audience it’s a thrill to be back in Springfield, her hometown. Principal Skinner steps out of the wings holding a big bouquet of flowers. Skinner congratulates Krellner on her success, pointing out that she always got A’s in school. Krellner responds that she did get a B or two in math, prompting Skinner to quip, “you are a girl.” The audience gasps, and Skinner tries to make amends, but only ends up making matters worse. The audience jeers, and some puppeteers armed with Itchy and Scratchy puppets kick Skinner in the crotch. Protestors show up at the school to voice their frustration. Superintendent Chalmers urges Skinner to do something. Skinner responds by addressing the protestors in a skirt. Try as he might to make amends, Skinner only ends up confusing and aggravating the crowd. Left with little choice, Chalmers steps in and announces that Skinner is being replaced by women’s educational expert Melanie Upfoot. Upfoot’s first order of business is to split the school in two, separating the boys from the girls. The crowd gasps.

Back at home Marge says that the uproar about girls and mathematics is ridiculous, and names a few of the things women have invented over the years. Homer angers her by listing many of the important inventions created by men. The next day Bart and Lisa make their way to Springfield Elementary. The interior has been redesigned to reflect its being split in two. Lisa and her classmates love the beautiful murals and art that adorn their part of the school. As Upfoot’s math class gets underway, Lisa is frustrated by the new approach, which emphasizes confidence building over real learning. Before long Lisa’s thirst for a real challenge gets the best of her. She makes her way to the boys’ school. She’s intercepted by Skinner, who has been demoted to Willie’s assistant. Lisa says it’s wrong that she can’t get the best math education just because she’s a girl. When Lisa returns home, she voices her frustration to Marge. Marge comes up with an idea: she dresses Lisa like a boy. The next day Lisa goes to school in her new disguise. She approaches Bart, who falls for the ruse. She tells Bart and his friends that her name is Jake Boyman, and quickly earns the nickname Toilet. A short time later Lisa takes a seat in her new math class, and is overjoyed by the challenging curriculum. Later, in the school commissary, Lisa infuriates Nelson by accidentally knocking over his tray of food. In the playground Nelson advances on Lisa as a bunch of boys gather around to watch the spectacle. Lisa thinks she has a chance of talking her way out of the fight, and even goes so far as to tell Nelson she loves him. When Bart returns home he discovers Lisa in her Jake clothes, disheveled and crying. Bart realizes that Lisa is Toilet.

Bart feels sorry for Lisa, and says he’ll teach her how to act like a boy. Bart’s “boy lesson” includes tips like eating French fries after they’ve fallen onto the floor, and picking a fight with someone who’s weaker than her. Lisa decides to hit Ralph on the arm. Ralph responds by sobbing and running away. Kearney and the other boys congratulate Lisa on a job well done. During the Student Achievement Awards Chalmers announces that “Jake Boyman” took top honors for outstanding achievement in the field of mathematics. Dressed as Jake, Lisa accepts the award and thanks the crowd. Then she pulls off her disguise, and announces that the best math student in the whole school is a girl. Bart claims that the only reason Lisa won is because he taught her how to think like a boy. Lisa denies this is true, and hurls her award at Bart, who ducks. The award hits Ralph on the head. Lisa says that although she did get better at math, it came at too great a price: abandoning everything she believed in.