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.

When Jorge and Berto hypnotize their principal into thinking that he is the superhero Capitán Calzoncillos, he leads them to the lair of the nefarious Dr. Pañal, where they must defeat his evil robot henchmen.

The Notebook of Doom is missing and Alexander and his fellow monster-hunters Rip and Nikki are convinced that the boss-monster has it. But is that monster the mysterious Principal Vanderpants--who is certainly behaving oddly--or someone else? They need to figure that out quickly because a mistake could have deadly consequences for Stermont Elementary.

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.

George and Harold hypnotize their principal who, believing he is the superhero Captain Underpants, leads them to the lair of the nefarious Dr. Diaper. They must then defeat his evil robot henchmen.

When George and Harold use their traveling purple potty to travel to another dimension where the school is nice and the principal, Mr. Krupp, thinks they're funny, they meet up with their evil twins and must face their cleverest enemies ever -- themselves.