There's trouble brewing in Bikini Bottom. Someone has stolen King Neptune's crown, and it looks like Mr. Krab, SpongeBob's boss, is the culprit. Though he's just been passed over for the promotion of his dreams, SpongeBob stands by his boss, and along with his best pal Patrick, sets out on a treacherous mission to Shell City to reclaim the crown and save Mr. Krab's life.

Burger Beard is a pirate who is 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 the entire city of Bikini Bottom is put in danger, SpongeBob, Patrick, Mr. Krabs, Squidward, Sandy, and Plankton need to go on a quest that takes them to the surface. In order to get back the recipe and save their city, the gang must retrieve the book and transform themselves into superheroes.

When his best friend Gary is suddenly snatched away, SpongeBob takes Patrick on a madcap mission far beyond Bikini Bottom to save their pink-shelled pal.

The story follows SpongeBob, as he travels to the depths of the ocean and faces off against the ghost of the Flying Dutchman.