
SpongeBob and Patrick get kicked off the bus for their antics and are back in Bikini Bottom. They learn that Sandy is building a rocket inside her treedome that can take them to Neptune's Paradise, leading SpongeBob to tackle numerous challenges so as to prepare for the flight.

SpongeBob needs his water helmet to enter Sandy's treedome. When he finds a sea snake resting in the helmet, he decides to use Squidward's clarinet to lure it out.

However, Squidward is in a deep sleep, so SpongeBob uses a pair of Dream Glasses to enter his dreams, where he is partially transformed into Squidward himself. SpongeBob convinces Squidward to give him the clarinet, which SpongeBob uses to retrieve his water helmet from the sea snake. Meanwhile, Patrick obtains the record for most sandwiches eaten at a diner. The gang then sets off again for Neptune's Paradise, but unbeknownst to them, Patrick accidentally breaks the oxygen pipe before the rocket tanks are completely filled. Sandy's rocket crashes in the affluent town of Bottoms Up.

SpongeBob then embarks on a search for oxygen fuel for the rocket, leading him on a quest to complete various tasks. Sandy instructs SpongeBob to get oxygen at Oxygen Springs Resort and Spa where geysers are used as hot-tubs but with bubbles of oxygen.

Each main level and side task will give the player a Goofy Goober Token once completed, and the player needs these tokens to learn certain skills and proceed to the game. Boss enemies include the giant frogfish from the film, Dennis (who is fought twice), and King Neptune. Four levels involve a boss enemy that the player must defeat to progress to the next level. Each level contains a main objective and side tasks. The player controls SpongeBob SquarePants and Patrick Star, both of whom have their own unique set of abilities. There are 18 levels in the game that loosely follow the storyline of the film. The gameplay is similar to that from Heavy Iron Studios' previous game, Battle for Bikini Bottom, as it was created using the same engine and shares many assets.
