Burger-Beard is a pirate in search of the final page of a magical book that makes any evil plan he writes in it come true, which happens to be the Krabby Patty secret formula. When his search is completed and the formula is missing, the entire city of Bikini Bottom is in danger. SpongeBob, Patrick, and the gang need to go on a quest that takes them to the surface.

In order to get back the recipe and save their city, they must retrieve the book and transform themselves into superheroes to fight Burger-Beard and his super villain pirate crew.