SpongeBob and Patrick are blowing bubbles when one grows large enough to carry them both into an underground cave. They navigate through it, avoiding ghost pirates, and discover the missing half of the ancient Atlantean Amulet — the object that Squidward, Sandy, and Mr. Krabs reveal can open the road to Atlantis. At Bikini Bottom Museum they join the two halves together. The path to Atlantis appears: a flying bus powered by song.
The bus crash-lands during travel. The group repairs it, arrives at Atlantis, and is welcomed by the Lord Royal Highness (LRH) for a tour full of hidden traps. Patrick manages to destroy the oldest living bubble in existence — twice — triggering a pursuit through Atlantean forces. Plankton, who had stowed away in the bus, has spent this time raiding the weapon rooms and emerging in a tank. His weapon fires ice cream. LRH captures Plankton as a replacement museum exhibit. An Atlantean soldier disposes of the amulet in a dumpster. The gang makes their way home.