The game begins with SpongeBob and his friends 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 mess. They began having a flashback that begins with them blowing bubbles until they get trapped in a big bubble that carries them into a cave. 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 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 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 in Patrick's part, forcing the gang to drive the bus around Atlantis to find the bus pieces and tool kits needed 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 had to avoid traps that were set around Atlantis for some 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. Unbeknownst to them, Plankton hid in the Atlantis bus compartment on the way here. He plans 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 to the weapon room. While taking pictures of attractions (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 again accidentally pops it for real, angering LRH. The group make a run for it, in which they must evade Atlantean forces while searching for paper clips to unlock doors. Later, Sandy uses Squidward as a gun to take down the soldiers. Plankton rampages around the city in his tank just like in the beginning and confronts the gang, ending the flashback. He fires his weapon, but is shocked to see it 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 to the national treasure of Atlantis. He then orders one of his soldiers to get rid of the amulet so that the troublemakers can't return. The soldier makes his way across Atlantis to the dumpster and tosses the amulet into it. The gang then heads home back to Bikini Bottom on board the bus.