The plot is divided into two sub-plots: the Right Side and the Wrong Side. The Right Side revolves around Spongebob trying to find Mr. Krabs to warn him about Planktons latest invention Robo Krabs. The Wrong Side revolves around Spongebob embarking on a quest to find Gary, who has been hidden somewhere in Bikini Bottom by Plankton and used to obtain the Krabby Patty formula.
The game consists of five different minigames, with them being played in a different order depending on which Side you play:
- Invasion of the Patty Snatchers: Play as Robo Krabs (Right Side)/Spongebob (Wrong Side) and assemble Krabby Patties by retrieving ingredients from sea ants.
- Boating School 101: Drive around the Boating School track and clear checkpoints of certain colors.
- Who Cut the Cheese?: Play as Spongebob and Patrick (Right Side)/Squidward (Wrong Side) and ride hooks to collect cheese.
- Hide N Go Jellyfishin: Play as Spongebob and Sandy (Right Side)/Patrick (Wrong Side) and capture jellyfish of certain colors to collect jelly.
- Save Me Money!: Stop the Flying Dutchmans pirate crew from stealing Mr. Krabss money by blasting them with bubble cannons.
The game itself has an impressive level of Continuity Porn, containing quite a few references from the first two seasons.
- Ability Depletion Penalty: Picking up the wrong color checkpoint in Boating School 101 or coming in contact with enemies like jellyfish, oysters, and electric eels in any of the games will reduce your time limit by a few seconds.
- Absentee Actor:
- Sandy does not appear in the Wrong Side.
- Gary does not appear in the Right Side.
- As Himself: All the canon characters are credited as themselves while the mentioned sea ants are given actual names.
- Attention Deficit... Ooh, Shiny!: The plot of the Right Side has Spongebob constantly getting distracted in his quest by hanging out with his friends.
- Big Bad: Plankton in both Sides, aided by an army of sea ants.
- The Cameo: Mermaid Man and Barnacle Boy are among the people sitting in the stands in Boating School 101.
- Continuity Porn: From the first two seasons:
- Hide N' Go Jellyfishin' and the blue jellyfish can be seen as a reference to "Jellyfish Hunter".
- The jellyfish Big Lenny from "I'm Your Biggest Fanatic" appears in Hide N' Go Jellyfishin' as an opportunity to capture and earn extra points.
- The Right Side features Robo Krabs from "Imitation Krabs".
- Who Cut The Cheese? Is one big reference to "Hooky".
- The pop guns from "Sandy's Rocket" are used to capture jellyfish in Hide N' Go Jellyfishin'.
- Patrick gives Squidward mouth to mouth like how he did in "Naughty Nautical Neighbors".
- When Patrick is seen running on top of a dock, he falls down similar to how he did in "Texas".
- Plankton's recurring exclamation of how he went to college is a reference to "Plankton!".
- Deadpan Snarker: The audio tape Plankton listens to in the Wrong Side.
- Dumb Muscle: The sea ants aren't all that bright, as they get Plankton's orders wrong and frequently fall victim to Poor Communication Kills.
- Eleventy Zillion: The last item Plankton tells Spongebob to bring him in the Wrong Side is one gazillion dollars, only for the tape he's listening to to tell him that there's no such thing, so he lessens it to just one hundred dollars.
- Fetch Quest: Plankton sends Spongebob on one in the Wrong Side in order to find Gary. The items include a learners permit, jellyfish jelly, Krabby Patties, cheese, and a hundred dollars.
- Tag Team:
- In Hide N' Go Jellyfishin', you can go behind Hideout Rock to reload your pop gun and switch between characters.
- In Who Cut the Cheese?, one character is selected to ride on a hook with no cheese while the other character collects cheese from other hooks before the former character reaches the surface.
- Villain Protagonist: You play as Robo Krabs piloted by Plankton in the Right Side version of Invasion of the Patty Snatchers.