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.

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.

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.

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

When we last saw our heroes, George and Harold, they had been turned into evil zombie nerds doomed to roam a devastated, post-apocalyptic planet for all eternity. But why, you might ask, didn't the amazing Captain Underpants save the boys from this frightening fate? Because Tippy Tinkletrousers and his time-traveling hijinks prevented George and Harold from creating Captain Underpants in the first place! Now, having changed the course of human history...

When George and Harold travel back in time to their kindergarten years, they are forced to relive the torment they received at the hands of a school bully. Unable to call on Captain Underpants for help, the boys try to find a way to outsmart the bully on their own.

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.

After being sent to jail for the rest of their lives, George and Harold are taken on a trip back in time by Tippy Tinkletrousers back to their Kindergarten days where they must deal with their bully without the help of Captain Underpants.

George and Harold are forced to contemplate a world without Captain Underpants.