The film begins with Painty the Pirate about to sing the television series theme as usual, but he instead pops out of the painting and throws the riders into Bikini Bottom. The audience ends up in the The Krusty Krab, where SpongeBob welcomes them and shows them how to make a Krabby Patty by pointing at the ingredients with his spatula. When preparing the Krabby Patty, SpongeBob accidentally loses a pickle. The pickle then bounces out of the restaurant into Patrick Star's hand on a pogo stick. Patrick steals the pickle. SpongeBob, while confused at Patrick's apparent betrayal, ultimately sets out to rescue the pickle, bringing the riders along with him on his bubble-bike. SpongeBob first rides out into town, wreaking havoc in the process, and eventually rides through Jellyfish Fields, where he is stung by a horde of Jellyfish. Suddenly, SpongeBob ends up falling into Rock Bottom, where a fish pops the bubble bike by biting it. The force of the pop hurdles SpongeBob into the air, landing in the Chum Bucket. It is revealed that the real Patrick had been kidnapped by Plankton, and the pickle thief was a high tech robotic version of Patrick. The robot then pursues SpongeBob, only to be unplugged by Patrick (looking for an electrical outlet for his toaster). Plankton is then crushed by his robot and SpongeBob recovers the pickle. Sandals enters the Chum Bucket to eat his patty; however, it turns out that Sandals is allergic to pickles. He swells up and then explodes. His head, eyes, and mouth land on his shoes and he runs out saying "I'm allergic to pickles." SpongeBob then laughs, saying "Well, that was pickle-culiar!".
This ride is a 3D motion simulator ride. Riders sit in a 3-D theater with chairs that rock and tilt along with the 3D movie.
Various effects are also used such as scents, water, wind, air blasts, leg ticklers, vibrations, strobe lighting, and smoke.
This is the last time in the series where the song Leaf Blower was used.
This ride stopped playing at the Nickelodeon Suites Resorts because of "SpongeBob 4D The Great Jelly Rescue".
There was a version of this attraction at Cedar Fair's California's Great America theme park located in Santa Clara, CA (before being bought by Cedar Fair Entertainment Co., it was owned by Paramount Pictures).