The game begins with SpongeBob and his friends in medias res escaping from Atlantis. Meanwhile, Plankton rampages around Atlantis with a tank he "borrowed" until he comes across the gang. SpongeBob and Patrick begin to remember how they got into this situation. They have a flashback that starts with them blowing bubbles until they get trapped in a big bubble that carries them into a cave (only the flashback is featured in the Nintendo DS and Game Boy Advance versions of the game, not the introduction). The duo make their way through the cave, avoiding ghost pirates while searching for ladders to venture deeper into the caverns, where they find the missing half of the Atlantean Amulet. Patrick thinks it is related to SpongeBob's ancestors because of the word "antis" on it. They bring it to the Bikini Bottom Museum to see what it is, taking pictures of exhibits and taking down tourists and security blocking the way. Squidward is shocked to see that they found the other half of the amulet. Sandy and Mr. Krabs tag along while walking in the museum. Squidward conjoins the two halves and the path to Atlantis is revealed: the path is a flying bus. The bus is powered by song, and the group starts to sing to get to Atlantis. The bus crash-lands along the way due to a mistake on Patrick's part, forcing the gang to drive it around the city to find the bus pieces and tool kits needed to fix it.