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 begin having a flashback that begins with them blowingbubbles until they got trapped in a big bubble that carries them into a cave. The duo makes 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.
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 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. 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, Patrick accidentally destroys the oldest living bubble and tells 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 and the group must 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 beginning 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 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 throw away the amulet so that the troublemakers can't return.
The soldier makes his way across Atlantis to the dumpster and tosses it in. Then the gang heads home back to Bikini Bottom on board the bus.
Nintendo DS version
At the beginning of the game, SpongeBob and Patrick are blowing bubbles. They blow one 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 have 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. The bus then crashes.
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 it is too dirty.
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 reaching Atlantis, Lord Royal Highness lets them explore it. 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 have to escape quickly. After fighting 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.
Idle Animations seen in the Nintendo DS version
SpongeBob - Sits on the ground and plays his nose like a flute. The same one in the Game Boy Advance version.
Patrick - Sits around and looks left and right and then chews on his hand.
SpongeBob SquarePants (Amulet Adventure, Snap Happy, part of Music Magical Journey, Bus Building Bonanza (technically in the bus), Tour Trouble, parts of Hide and Sneak)
Sandy Cheeks (part of Music Magical Journey, Bus Building Bonanza (technically in the bus), parts of Tour Trouble, Money Krabbing, parts of Hide and Sneak, Squidward Super Shooter)
Patrick Star (Amulet Adventure, part of Music Magical Journey, Bus Building Bonanza (technically in the bus), parts of Tour Trouble, Paparazzi Patrick, parts of Hide and Sneak)
Squidward Tentacles (part of Music Magical Journey, Bus Building Bonanza (technically in the bus), parts of Tour Trouble, Squidward the Poser, parts of Hide and Sneak, Squidward Super Shooter (technically the gun)
Eugene H. Krabs (does not speak) (Bus Building Bonanza (technically in the bus), parts of Tour Trouble, parts of Hide and Sneak)
Sheldon J. Plankton (Tanklantis Plankpantis in a tank), part of Music Magical Journey, Bus Building Bonanza (technically in the bus, but does not speak), Armory Antics, Super Tank Showdown (in a tank)
SpongeBob (Tanklantis Plankpantis, part of Music Magical Journey, Money Krabbing, Paparazzi Patrick, Armory Antics, Operation: Trash Dash)
Sandy (part of Music Magical Journey, part of Tour Trouble, Armory Antics, Operation: Trash Dash)
Patrick (Tanklantis Plankpantis, part of Music Magical Journey, part of Tour Trouble, part of Money Krabbing, Armory Antics Operation: Trash Dash)
Squidward (part of Music Magical Journey, part of Tour Trouble, Money Krabbing, Armory Antics, Operation: Trash Dash)
Mr. Krabs (Snap Happy, Music Magical Journey, part of Tour Trouble, Money Krabbing, Armory Antics, Operation: Trash Dash)
This commentary is an unlockable feature that goes with each level. It reveals with-in the universe behind-the-scenes content provided by SpongeBob, the director of the game. It reveals that the game is not a video game version of "Atlantis SquarePantis," but based on the events of it.
An IGN review of the Nintendo DS version was headlined, "SpongeBob actually managed to be boring." Likewise, the most-criticized aspects of all versions were the clunky camera control, the lackluster AI, and the annoying method of having to return to the start of the level to switch characters. It was also called "too short" and "too easy" for older gamers. A review of the Wii version called the game "second-rate," "sloppy," "tedious" and "really boring." The graphics were criticized for being "bland." The PlayStation 2 version was criticized for the same reasons but was given a slightly lower rating because IGN says that Wii Remote controls spice up the shooting games.
All versions of this game have backward compatibility.
The PlayStation 2 version can be played on old PlayStation 3 units.
The Game Boy Advance version can be played on all DS and DS Lite units.
The Wii version can be played on all Wii U units.
The Nintendo DS version can be played on all 3DS/2DS/DSi units.
There are only two platforming stages in the game. The game has mostly "point and shoot" and button combination stages.
Mr. Krabs is bright red in the PlayStation 2 version.
Mr. Krabs doesn't speak in this game; he only makes groaning and laughing sounds.
Just like what happened with Creature from the Krusty Krab, the Wii version's disc used two ink colors at launch, but eventually was given the PlayStation 2 printing but with Wii insignia.
In the episode, they never stop in the lost continent of Mu to refuel, which only happens in the Nintendo DS version of the game.
However, in the Game Boy Advance version there is a minigame where the player battles Atlantean guards, but in the cutscene after the minigame, LRH says that Sandy has been captured when she defeated all the guards.
Also in the Game Boy Advance version, the final boss is Giant Plankton, another thing different than the TV special.
The voice of some of the Atlanteans was the same voice as the Professor from the Alaskan Bull Worm in Creature from the Krusty Krab.
The voice of the narrator in the first cutscene was the same voice as the Helicopter news correspondent in Creature from the Krusty Krab.
In the introduction, a portion of the menu music in Creature from the Krusty Krab can be heard in the background.
In the Amulet Adventure! level, SpongeBob names the cave "Dave."
According to SpongeBob, before this game, Patrick has had hunted bread products at least once.
In the "Amulet Adventure!" level, it foreshadows SpongeBob and Patrick finding the amulet twice. The first time is when SpongeBob wonders if there is a treasure in the cave and the second time is when the Ghostly Pirates mention that there is a treasure in the cave.
SpongeBob almost breaks the fourth wall thrice. Once in Snap Happy!, when he wishes that he could continue to take pictures by wishing that this adventure was a game. Once in Tour Trouble!, when he says that being in the Science Room is like being on a TV. Once in "Money Krabbing!" in the commentary when he mentions that he should have a TV show, but then thinks that that would not be a good idea. He then asks, "Who would watch a show called, 'SpongeBob SquarePants?'"
The producers for the console versions, Team RocFISH, hid RocFish in every level of the game and in some of the variations of the levels too. They are:
Tanklantis Plankpantis! - ?
Amulet Adventure! - They appear below the platforms.
Snap Happy! - At the end of the level, a RocFish appears outside of the Museum.
Music Magical Journey! - They appear outside of the bus.
Bus Building Bonanza! - ?
Tour Trouble! - ?
Money Krabbing! - It sometimes appears as one of the objects going down from the top of the screen.
In the Nintendo DS version, the Flying Dutchman's ship from "Shanghaied" is seen when Patrick & Mr Krabs are trying to get the blue crystal. Also in the console version the player can see the Flying Dutchman's head in the first section of the "Snap Happy!" level.