The plot follows a pirate named Burger Beard (Antonio Banderas), who steals the Krabby Patty secret formula using a magical book that makes any text written upon it come true. After Bikini Bottom turns into an apocalyptic cesspool and the citizens turn against SpongeBob, he must team up with Plankton to find the formula and save 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.

After King Neptune's crown is stolen, SpongeBob and Patrick go on a quest in 6 days to retrieve his crown. On the way SpongeBob and Patrick defeat many evildoers using their brains and bronzes. While this is happening someone is taking over Bikini Bottom and SpongeBob and Patrick must defeat this mastermind.