Only Captain Underpants can stop the space aliens who have turned everyone into lunchroom zombie nerds.

Having changed the course of human history after unwittingly wondering what could be worse than going to prison, George and Harold are catapulted through time back to their kindergarten days, where they are subjected to a sixth-grade bully and a clueless school principal.

Harold and George's time-traveling Purple Potty lands them in an alternate universe where everything seems delightful, but evil lurks just beneath the surface, and leads to a battle between Captain Underpants and his own evil twin.

George, Harold, Captain Underpants, and Sulu the Bionic Hamster battle the three Ridiculous Robo-Boogers in an attempt to turn the Bionic Booger Boy back into Melvin Sneedly.

The monstrous Turbo Toilet 2000 is determined to take revenge on George, Harold, and Captain Underpants.

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.

When Professor Pippy P. Poopypants comes to Jerome Horwitz Elementary School to teach science, and he goes off the deep end because students make fun of his name, only Captain Underpants can save the school from the professor's perilous plot.

When the teachers of Ella Mentry School go on strike, A. J. and the gang meet a new principal who does not believe in rules and says that the students do not have to learn anything if they do not want to.

When the new vice principal is put in charge of Ella Mentry School for a few days, she tries out some very unusual ideas about how students learn.

Tired of following the strict rules of their grumpy replacement principal, second-grader A.J. and his classmates try to find a way to bring back eccentric but lovable Principal Klutz, who was fired for bringing a wild turkey to the school's Thanksgiving Day assembly.