After women of Springfield criticize Principal Skinner because he thinks girls are bad at math, the school is divided into boys and girls, but the math class for girls doesn't teach real math, so Lisa disguises as a boy to infiltrate into the boy math class.
The Simpsons and many other prominent Springfieldians go to see a performance of Stab-A-Lot: The Itchy and Scratchy Musical. The show pretty much comprises the homicidal cat and mouse doing what they do best, but all in song. The audience is enthralled by the performance and give it a standing ovation. Julianna, the director comes out on stage, accompanied by Principal Skinner, to acknowledge the cheers. Skinner reveals that she used to be a student of Springfield Elementary and, while acknowledging all her accomplishments, when Julianna points out she got a B in math,Skinner then says "you are a girl". Whether he intended something else or not is unknown, but expectedly, everyone in the audience - women, in particular - are shocked.
The next day, the teachers of Springfield Elementary and other ladies stage a protest outside the school against Skinner's remark, much to the displeasure of Superintendent Chalmers. Skinner assures him that he will take care of it and holds a conference in the school's auditorium, inviting all the protesting ladies to attend. There, he tries to pacify them - by wearing a skirt (revealing his hairy legs), much to the amusement of his students, but not the ladies. He tries saying that men and women are equals, but unique. Nothing he says has a good effect on the ladies, so finally he starts hyperventilating and collapses on stage. Chalmers comes out and introduces them to their new principal - a lady principal, that is. As her first act as principal, Melanie Upfoot separates the boys and girls into separate schools. The move is met with mixed reactions. Principal Upfoot seems to be even more gender biased than Principal Skinner, having done up the girls' half of the school to be beautiful, clean and have paintings in the hall while letting the boys' side end up looking like a war zone.
The next day, Otto drops off the girls at their school, and then drives a few feet ahead and releases the boys from their cage in the bus, so they can attend their school. Lisa seems to feel right at home in the girl-friendly school, with the fountains, paintings, pink paint and all. She attends math class, which will be taught by the new principal herself. However, instead of usual number-crunching or the like, she starts speaking about the philosophy and magic in math. While the other girls enjoy it, Lisa asks whether they will get down to doing problems, to which the principal replies that is how boys look at math. Disillusioned by this pro-female bias toward one of her favorite subjects, Lisa walks out and gets into the boys' school compound. She peeps into one of the classrooms and sees a math class in session, where actual, accurate math is being taught (exactly how she likes it). She is caught by Skinner, now an assistant to Groundskeeper Willie and told to leave.
After a chat with Marge, she decides to disguise herself as a boy, named "Jake Boyman" and attend the boys' school (Everyone calls her "Toilet", due to first appearing with toilet paper on her shoe). During the math class, she gets a problem wrong, but she feels happy to have learned something. Unfortunately, being with the boys means having to act like one. She gets into a fight with Nelson and, as much as she tries to use her intelligence to escape her situation, she gets beaten up.
When Bart returns home that day, he walks up to Lisa's bedroom door laughing and tells her that she missed Nelson pounding a "dweeb". However, his impression of the fight becomes more tragic and upsetting rather than funny when he sees Lisa, still dressed as Jake, bruised and dirty, sitting on her bed, crying quietly. He feels sorry for her and he tells her that he will teach her to act like a boy.
Thanks to Bart's help, she starts acting more like a boy, including beating up poor Ralph Wiggum. However, she does well in math class. Finally, at an award ceremony, "Jake" wins an award for outstanding performance in math. Lisa then reveals her identity to the whole school, and explains why she had to disguise herself. Bart gets up and tells everyone that she did well only because she was acting like a boy. Angry at hearing this, she throws her award at Bart, but ends up hitting Ralph. Shocked at how "boy-like" she has become, she apologizes to Ralph. However the boys embark in a chair fight as Lisa claims she did well in math and then beats up Martin with a chair. In the end, it is assumed that Skinner is reinstated as principal.
Itchy, Scratchy, Itchy, Itchy, Scratchy Itchy, Scratchy, Itchy, Itchy, Scratchy From the day you are born in the alley To the day you are hit by a car There's cream to drink And mice to eat And great big balls of yarn It's the circle... The circle of...knife.
[Sung by Itchy and Scratchy] Scratchy: I don't know why I trust him I guess some cats just never learn Itchy: I feel so good when I have crushed him Or left him mangled, maimed, and burned Both: I supposed it's symbiotic And perhaps a bit erotic Scratchy: 'Cause pain is my narcotic Itchy: You really liked it? Scratchy: Yes, I loved it Both: And that's why we're always... Itchy: Fighting Scratchy: and Biting Itchy: And dynamite igniting