Spongebob and Friends have left Camelot after their Quest to cure Cynder and find Spyro and some new members have joined their team. They are on a quest to find Atlantis. the city of Atlantis is threatened by Dark Cynder, who casted a huge tidal wave that will destroy the whole city. In order to protect the city, the queen of Atlantis offers herself as a sacrifice to The Heart of Atlantis, hovering above the city. The The Heart of Atlantis then surrounds the main part of the city with a force field-like shield, protecting it against the tidal wave as the city is sunk to the bottom of the ocean.
few Adventures later, Milo James Thatch (Michael J. Fox), an aspiring young linguist working in the boiler room at the Smithsonian Institution in Washington D.C., believes that a manuscript known as the Shepherd's Journal will lead to the location of Atlantis. When his request to lead an expedition is denied by the Institution's board, he finds himself contacted by millionaire Preston B. Whitmore (John Mahoney), a friend of Milo's late grandfather, Thaddeus Thatch. The elder Thatch had already located the Journal, and asked Whitmore to give it to Milo “when he was ready.” Whitmore asks Thatch to become part of a team to search for Atlantis on a high-tech submarine led by Commander Rourke (James Garner) and his second-in-command Helga Sinclair (Claudia Christian). The team’s sub is sunk by the Leviathan, a huge, ancient mechanical lobster-like monster. The team escapes with heavy casualties, and find their air pocket entrance to Atlantis. Just before reaching Atlantis, our heroes used the airship to go by the posable hazards surface. To their amazement, the city still survives in a bubble beneath the earth.
Atlantis’s princess, Kidagakash (Cree Summer) (nicknamed “Kida”) greets them and brings them to her father, the king of Atlantis (Leonard Nimoy), and her Uncle, Lord Royal Highness, who is more welcoming, unlike his brother, and had Cynder, Spyro, and Even Sparx arrested and let's the others stay. but eventually allows them to stay for the tour Kida takes Milo on a tour of the city, and they explore an underwater mural which leads Milo to discover that the Heart of Atlantis, which he originally believed to be a power source, is also what is keeping the whole city alive. When they resurface from the mural, however, Milo finds out that the crew intends to take the Heart of Atlantis to the surface and sell it (thinking that it is some sort of crystal); when he refuses to work with them, Rourke forces Milo’s cooperation by threatening Kida’s life,
but Lord Royal Highness orders for the royal guards, most were defeated by chrome claw, who was later defeated by Vinny, tigress, Master Shifu's student, throws Helga off to save Milo, and to get back at her cause Helga called Tigress ugly. and Seadramon uses its ice attack to hit Rourke’s arm, crystallizing the commander.
Plankton had the displasure of becoming the 3rd natiional tresasure of atlantis, being the other two the cystail, and the worlds oldest bubble
The city safe once again. The crew prepares to return to the surface with riches given to them by the Atlanteans, but Milo, who has fallen in love with Kida, chooses instead to stay behind in the city. The team, once they return to the surface, and Mr. Whitmore come up with an alternative story to protect Atlantis’s secret and give Mr. Whitmore an Atlantean crystal;allowing him to be given the same life extending force that the citizens of Atlantis have. Milo and Kida, now king and queen of Atlantis, carve a stone likeness of the late king, which then ascends to join the other stone carvings of past kings circling the Heart of Atlantis (now once again open to the people of Atlantis, rather than hidden underground), and look upon the city as it begins to return to its former glory. As for the shell lougers, they find that their battles are far from over, as Kairi is in danger once again, but they are prepared.
None (it actselly does, but not in the movie, songs from the atlantis squarepantis, and the villain song from the Proud Family movie.)
- This introduced Spyro, Sparx, and Cynder from the Spyro games, Brandy and Mr. Whiskers, Sam and Max: Freelance Police as new friends of Spongebob.
- 2 updated laugh sequences features Private, Skipper, Kowalski, and Rico laughing at Mr. Whitmore's humorous picture before Bagheera says, "It's not funny." The other one features Iago laughing at Mole.
- When Milo and the Shell League Squad meet Rourke, Rourke mentions Camelot.
- Max the Cat, Sora, Donald, and Goofy guest star in this film.
- After the leviathan is spotted on the scope, Kowalski shouts to fire all weapons. They believe that they killed it and they find out that they hit an old tire. Private says that on the sonar, they all look the same. Skipper says that he'll fudge the whole mishap. Private asks Skipper about when he said that when they destroyed the snakehead.
- In the original film, Milo and the crew go through mishaps such as running into a big bug and others is omitted. In its place, the Shell Louge Squad travel the rest of the way via the Shell Louge Squad's SkyShip to Atlantis. After crash-landing, Icky asks why all the original stuff was omitted. Banzai explains that SuperVideoManiac2 thought it would be easier to find Atlantis if they used the SkyShip. Squidward says that he delayed too much on the 1st four parts.
- The final battle takes place in the throne room instead of the volcano shaft.
- The Atlantis crew says that they DID find Atlantis and that Rourke and Helga were Villain Leaguers. Rourke was frozen by Seadramon and Tigress struck Helga over an edge.
- Vinny defeats Chrome Claw by throwing a Dynamyte at a bridge.
- The king dies after the Shell Lougers left.
- At the end, Ignitus and Terrador arrive to warn the Louge that Kairi is in danger. Spongebob summons the monsters of Monsters vs. Aliens to help them in their future adventures. but for the current project of Spongebob and friends meet the great mouse dectecive, he will get the help from the atlantis team. along side with Simba, Toothless, a night fury, and Hiccup, toothless's master.
- The audio for when Squidward and Shenzi say "Say what?!" is from Family Guy and Clone High.
- an unathotised preview of the Porject can be seen on another channel, held by a local trouble maker too allow hacklers to hackle.