Kang and Kodos had invaded Springfield and used a laser to cause dolphins to attack humans. They have taken over the Squidport, where Bart and Lisa free Captain McCallister, who was attached to a post by the dolphins. He gets in his boat and heads to a hatch while Bart and Lisa make their way across the pier beating dolphins. When they enter, Lisa uses the "Hand of Buddha" to make a bridge dropping billboards on the water so they can get past a boathouse. Then, she uses the Buddha's Hand power flick to throw the dolphins to a big ship and make it fall to the water so Bart and Lisa can jump on it and get to another pier.
They enter a wooden tunnel and get to a big fast spinning octopus-shaped wheel (which makes Bart and Lisa fall if they approach it), where a door that leads to the pipe is locked. When they defeat all the dolphins, the door opens. Bart and Lisa see King Snorky, the dolphin king, kidnap the Captain and jump into the pipe so they jump on the Captain's boat to get to it. Now they are inside the dolphins giant cave, full of shells, oysters, starfishes and big pools and aquariums.
King Snorky is on the top of an oyster above an aquarium. Lots of dolphins come from the three aquariums, two of which can be closed to reduce the number of dolphins. Bart can use his slingshot to shoot at the oyster and make King Snorky fall to the water, but he immediately gets up again. To defeat him, Lisa uses the Buddha's hand to make a way up some rocks to another meditation point using giant trampoline jellyfishes. When she gets to that meditation point, she uses the Budha's Hand again to place an electric eel inside King Snorky's aquarium. Now when Bart shoots at the oyster, King Snorky falls to the water and dies.
Captain McCallister then thanks Bart and Lisa, almost breaking the fourth wall in the process, while Kang and Kodos look them from their spaceship, eating egg rolls.
Bart: Bart is one of the playable characters, he can jump, kick, use his slingshot, open his cape to release bats and turn into Bartman to glade, climb walls and ziplines and grapple. He can also turn into Robo-Bart (only in the Xbox version).
Lisa: Lisa is one of the playable characters, she can jump, kick, play her saxophone to stunt enemies and use the Buddha's Hand to pick up and drop big things and kick enemies from above. She can also turn into Clobber-Girl (only in the Xbox version).