Springfield is in an uproar after Principal Skinner makes a sexist comment at the end of an Itchy and Scratchy musical. Principal Skinner is replaced by Melanie Upfoot, a women's educational expert, who decides to divide the school into two different schools: one for boys, and one for girls. Studious Lisa soon becomes frustrated when she isn't learning anything from "girls' school." When the Principal refuses to allow her to take math at the boys' school, Lisa decides to dress up as a boy. While Bart teaches her the ropes of boyhood, Lisa wins the math award at the Student Achievement Awards and learns what it's really like to be a part of the "boys' club" .

After visiting an evolution exhibit narrated by guest star Griffith, Flanders pushes Mayor Quimby to appoint Reverend Lovejoy as a "Mortality Czar" in charge of spreading the theory of creationism. Darwin's theories are quickly outlawed and Lisa finds herself as the only supporter of the scientific theory. After holding secret evolution classes, Lisa is arrested and retains Southern lawyer Wallace Brady to help defend her beliefs in front of a judge. While Flanders is on the stand in court, Homer's antics cause him to crack under pressure and he calls Homer an ape, which leads the judge to believe Homer resembles the missing link - putting a monkey wrench in the prosecutors' case. Blackboard: 'Je ne parle pas Francais'.