When George and Harold hypnotize their principal into thinking that he is the superhero Captain Underpants, he leads them to the lair of the nefarious Dr. Diaper, where they must defeat his evil robot henchmen.
While Raven is away, Luca breaks his promise to her and returns to the Wish Library, asking to be in charge at school, but being principal for a day is not all fun and games.
Professor Pippy P. Poopypants comes to Jerome Horwitz Elementary School to teach science, and goes off the deep end because students make fun of his name, leaving Captain Underpants to save the school from the professor's perilous plot.
A snotty situation ensues when Melvin Sneedley, an academically-gifted student, turns into the Bionic Booger Boy and must be stopped by George, Harold, and Captain Underpants.
Captain Underpants and his friends, having dispatched Melvin Sneedley, the Bionic Booger Boy, must join the fray again when they realize they have forgotten about Sneedley's sidekicks, the Robo-Boogers.
Crackers and Sulu, the Bionic Hamster, finds themselves in a backwards universe where George and Harold's own evil twins rule the school with the help of the wicked Captain Blunderpants.
When George and Harold hypnotize their principal into thinking that he is the superhero Captain Underpants, he leads them to the lair of the nefarious Dr. Diaper, where they must defeat his evil robot henchmen.