The game begins with SpongeBob and his friends escaping from Atlantis. Meanwhile, Plankton rampages around Atlantis with a tank that he stole until he comes across all of them. SpongeBob and Patrick begin to remember how they got into this mess. They begin having a flashback that begins with them blowing bubbles until they got trapped in a big bubble that carries them into a cave. The duo make their way through the cave, avoiding ghost pirates and searching for ladders to venture deeper, 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 take 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 Cheeks and Mr. Krabs tag along while walking in the museum. Squidward combines the two broken halves of the amulet and the path to Atlantis is revealed; a bus.
The bus is powered by song, and the group starts to sing to get to Atlantis in which the bus crash lands along the way, forcing them to drive the bus around Atlantis to find the bus pieces and toolkits to fix the bus.
After repairing the bus and arriving at Atlantis, the group is greeted by the Lord Royal Highness (or LRH). LRH gives them a tour around the Atlantean palace in which they have to avoid traps that were set around Atlantis for some unknown reason. Mr. Krabs begins to collect some treasure to take with him with some help from Sandy and her bubble catching gun. Squidward poses for the artists in the art studio. Unbeknownest to them, Plankton hides in the Atlantis bus compartment on the way there. His plans are to use the Atlantean weapons, the most advanced of all time, to destroy SpongeBob and his friends, and take over the world. After getting out of the bus, he sneaks around Atlantis and makes his way into the weapon room.
While taking pictures of attractions and also taking down tourists and Atlantean guards blocking the way, Patrick accidentally destroys the oldest living bubble and tell the truth to LRH who shows them the real bubble. Squidward reminds them that the bubble that Patrick destroyed was a prop for tourists. Patrick then accidentally pops the real bubble and the group run from Atlantean forces, searching for paper clips to open doors. Sandy uses Squidward as a gun to take down the soldiers.
Plankton rampages around the city in his tank just like in the opening part of the game and confronts the gang in which ends the duo's flashback of how they got here. He fires his weapon, but is shocked to see it just shoots ice cream. LRH captures Plankton, believing he is a talking speck, and displays him as a replacement for the recently destroyed bubble and as a replacement for the national treasure of Atlantis. He then orders one of his soldiers to throw away the amulet so that any troublemakers can't return.
The soldier makes his way across Atlantis to the dumpster and tosses it in. Then the gang head home back home to Bikini Bottom on board the bus.
The game begins with SpongeBob and Patrick blowing bubbles. They blow a bubble that is too large, and they get trapped inside it, taking them to a cave. In the cave, they discover parts of the Atlantean Amulet. After finding all ten pieces, the cave begins to collapse, and they must escape. After leaving the cave, the two go to to save Bikini Bottom from an army of Ghost Jellyfish and show the Amulet to Squidward at the museum. He realizes that by finding the Amulet, they can go to Atlantis.
They want to take Mr. Krabs, who agrees, but makes SpongeBob and Patrick find his golden spatula first. After finding it, they try to get Sandy to come with them, who agrees under the condition that SpongeBob and Patrick defeat her in a karate match. After defeating Sandy, they head into the bus and fly to Atlantis, but run out of song fuel and crash.
They discover that they are in the lost continent of Mu. The leader of Mu tells them that they can find sheet music for Squidward to play there, but they need to find the red and blue jewels to be able to access it in the ruins of Mu. They find both jewels and fight a boss for the sheet music, but they discover that it is too dirty to read.
They head into the volcano to find a sacred fire flower that can make the music readable. Upon finding it, Squidward's clarinet has been stolen by a giant jellyfish, but they manage to recover it. Squidward plays the sheet music, providing the song fuel needed to reach Atlantis.
After finally reaching Atlantis, Lord Royal Highness lets them explore. They travel through the treasure room, a science lab, a music room, and an industrial factory before they finally reach the world's oldest living bubble.
Unfortunately, SpongeBob and Patrick pop it and the Atlanteans turn on them, forcing the two to escape quickly. After a fight through the Atlantean guards, they reach the courtyard of Atlantis, where Plankton pops out. They destroy Plankton's tank and return home to Bikini Bottom.