The show begins with SpongeBob blowing bubbles and Patrick taking pictures of them, causing them to pop. Patrick then destroys the camera, saying it is not fast enough. SpongeBob thinks it is the very nature of the fragile bubble. He then sings a song about bubbles, then accidentally blows a larger bubble than expected and is unable to pop thanks to the Extra strength bubble liquid. It lifts SpongeBob and Patrick off the ground and they eventually float into a cave. Then, a broken coin pops the bubble. Patrick assumes the amulet belonged to SpongeBob's ancient ancestors . They take it to the Bikini Bottom museum to see if the staff there know what it is. There, Mr. Krabs sets up his own admission booth, but soon takes it down when a person who he cheated of money complained to a Museum security guard. Patrick and SpongeBob run into Squidward, who was busy painting. Squidward thinks SpongeBob and Patrick stole the missing half of the Amulet. He soon matches it to the displayed other half of the Amulet. Then, Mr. Krabs, interested in the untold riches, runs into Squidward, who tells Mr. Krabs how the streets were paved with gold and street lights made of diamonds . Squidward teaches Mr. Krabs, SpongeBob and Patrick about Atlantis, its origin and other things, including the Oldest Living Bubble, to SpongeBob's delight. Sandy, who overheard them, steps in, mentioning Atlantis' science. Sandy, Patrick, Mr. Krabs and SpongeBob convince Squidward to link the two halves together since if the two halves were joined, the path to Atlantis would open.
The magical path is opened. The captain tells the group to refill fuel, but he reveals the fuel as song . The group sings about their desires. Plankton sneaks on wanting to use Atlantis's powerful weapons to become king of the city. Patrick at last, causes the bus to crash by singing his own song and stops in the middle as he does not know what he likes when he says that part. The bus crashes in to a topiary garden in Atlantis. There, they meet the Atlantean King, Lord Royal Highness , who shows them a grand tour of the fortress. During the tour, Mr. Krabs, Sandy and Squidward each get distracted by places in Atlantis; Mr. Krabs unsurprisingly by the treasury room, Sandy by the science lab, and Squidward by the art gallery. Each sings their own song about how much they love Atlantis.
Meanwhile, Plankton checks out the Weaponry Room. He then chooses his weapon, a tank. Finally, SpongeBob and Patrick get to see the world's oldest living bubble alive, over 1 million years old. They take a picture of it, which causes the bubble to pop. They are afraid to speak, saying they have to go back to Bikini Bottom . Then, Patrick shouts out the 'truth' ("WE DESTROYED YOUR MOST PRIZED POSSESSION!", "It's not a joke! We burst the Bubble!").
Lord Royal Highness is not mad at SpongeBob and Patrick for popping the bubble, saying that the one they popped was just a tourist attraction ("That's not the real bubble! It's just a prop for the tourists."). He then shows them the real oldest living bubble, but once again, when Patrick takes a picture of it, it pops. Angered, Lord Royal Highness summons the Atlantean Royal Guard to attack, but the gang manage to escape . Just when they escape outside with the royal guards still in pursuit, Plankton comes in and tries to destroy them with the tank he found, but it showers the group with strawberry ice cream, much to Plankton's dismay ("Ice cream? It shoots ICE CREAM?!"). Lord Royal Highness picks Plankton up saying that a "talking speck" would be a better replacement for the bubble. Lord Royal Highness removes the Amulet from the bus and orders a royal guard to dispose of it. SpongeBob is ready to go home, but Patrick, Sandy, Mr. Krabs and Squidward all cry because they want to stay in Atlantis; even though SpongeBob does not.