After receiving the tickets to Neptune's Paradise, SpongeBob first serves a Krabby Patty for a grumpy customer and then is informed by the customer how to get to the park; to take a bus there. After his shift at the Krusty Krab is over, SpongeBob heads downtown where he meets Patrick to board the bus. Unfortunately, SpongeBob does not have money for bus tokens. SpongeBob goes to Goo Lagoon, the local beach, to find the Flying Dutchman's buried treasure to pay for tokens. After SpongeBob completes a series of tasks for various characters, he finds the Flying Dutchman's treasure, which is a chest entirely full of bus tokens. After SpongeBob completes several more tasks in order to convince a bus driver to agree to take them, he and Patrick depart for Neptune's Paradise.
Chapter 2: Hitting Rock Bottom
SpongeBob and Patrick, end up in Rock Bottom due to heavy rain, and the bus driver gets upset with SpongeBob and Patrick for getting him trapped there. He refuses to help SpongeBob any further until the weather clears up and SpongeBob gets left on his own. SpongeBob eventually learns that the rainstorm is being caused by Marlin the wizard, who is upset at a local weatherman for wanting to build a machine that can control the weather. Marlin feels threatened by the machine since controlling the weather is his job. After SpongeBob and Patrick destroy the weather machine, Marlin stops the rain and the pair continue their travel to Neptune's Paradise. However, the bus driver gets irritated more than he can handle with SpongeBob and Patrick's childish antics and eventually tricks them into getting off the bus before he drives away.
Chapter 3: Back to Square One
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.
Chapter 4: Bottoms Up!
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. However, the intercom denies SpongeBob access to the springs on the grounds that SpongeBob is not wearing a jacket. So the pivotal point of this chapter is SpongeBob must find a jacket from somewhere to get into the springs. Meanwhile, Patrick searches for a bathroom after eating junk food in the previous chapters. After a series of tasks to get his jacket, SpongeBob ends up traveling to a small wealthy city, Waverly Hills where he finds himself at a very fancy seafood restaurant inside of the wreck of the Titanic. SpongeBob receives a loaned jacket at the restaurant but is then kicked out after he accidentally reveals that he is from Bikini Bottom, a town that the waiters of the restaurant dislike. Luckily, the waiter forgets to take back SpongeBob's jacket. After successfully getting into the Springs, and refilling the oxygen tanks, they leave for Neptune's Paradise before the park is closed.
Finale
The gang gets to Neptune's Paradise, but an employee tells them that the park is closed for a private party. SpongeBob and Patrick are sad initially, but Sandy tells the employee that it is their party, and they are allowed to enter. Inside the park, they meet all of the characters they met along the way, who seemed to have planned this for SpongeBob. They all then enjoy the rides and attractions.