Principal Krupp once again turns into the superhero Captain Underpants in order to save the world, and Jerome Horwitz Elementary School, from the evil talking toilets and the Turbo Toilet 2000.
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.
Having changed the course of human history after unwittingly wondering what could be worse than going to prison, George and Harold are shot through time back to kindergarten, where they are subjected to bullying and a clueless school principal.