The opening intro for the game features Calamitous on some sort of game show (which is called the Biggest Genius). Professor Calamitous states that by feeding fairies the Krabby Patties, they can emit a gas that, combined with Ghost Energy, can be used as a form of fuel for his army of the Toybots.
The game itself opens with SpongeBob and Patrick delivering a truckload of several million Krabby Patties to a Krabby Patty processing and toybot factory. Upon arriving at the factory, A robot sucks up all the Krabby Patties, and Patrick unintentionally in the process. SpongeBob chases after the robot, SpongeBob disguises himself as a robot to get into the factory, and save Patrick.
After finding his way through the factory, SpongeBob finds Patrick vacuum-packed like a toy. After freeing Patrick, he meets Tak, who claims to have been abducted and scanned. They later find Timmy, Cosmo, and Wanda. Since Cosmo and Wanda ate too many Krabby Patties, they aren't able to wish the factory away, but can still protect the heroes from harms way.
They later find Jimmy who also claim to have been abducted and scanned. They meet the Chadbot, a robot who is Calamitous' helper. They ask him to use something to contact Danny Phantom and commands them to find more master models for his collection.
After collecting the master models, Jimmy contact Danny who says that Calamitous, invading toy army took over his house to use he energy coming from the Ghost Zone so Jimmy tells Danny and Sam to meet him and the other Nicktoons at the Amity Park (which is almost destroyed) EvilToyCo outlet and when they get there they see Jimmy made some mech-suits that will let them fight the big tin robots. After defeating a giant evil toy Jimmy head, they head back into the factory where they find some more master models.
Chad-Bot tells them that Saucer Men toys capture heroes, so the Nicktoons go through the factory, collecting the rest of the master of master models, and destroy the Saucer Men toys, then the Nicktoons head to Fairy World. They then free Jorgen (who was in a frozen state on till Patrick bumped into him thanks to Jimmy), who destroys the fairy harvester, and then get back into the mech-suits to the Professor's lair (Jorgen even tells them to collect 500 fairies which they do).
They get to where the opening into of the game was and the winner of the Biggest Genius is none other than Chad-Bot himself who tells Calamitous, plan to abduct the best characters from every universe lead to his victory and the game ends with Chad-Bot cutting Calamitous, mustache off with a electric shaver.
|Name||Home Console||DS||Unlockable||Special Costume|
|Patrick Star||Barnacle Boy|
|Timmy Turner with Cosmo and Wanda||Cowboy|
|Jimmy Neutron||Secret Agent|
|Danny Phantom||Dan Phantom|
|Sam Manson||Plant Girl|
|Stimpy Cat||Kited Yaksman|
|Jenny (XJ-9)||Flame Colored|
- Professor Calamitous
- Mr. Huggles
- Exo-Huggles 3000
Before each level you can select two characters as who you want to play as in the level. However in the special levels in which you control a mech-suit you can only select from the default characters. In the handheld version everyone can enter a mech-suit during the level when reached it.
In the game there are several special things you can collect called the Master Models. Chad-Bot asks if the heroes can collect these Master Models for some reason, not telling them Calamitous needs them. Some of the Master Models appear as playable characters like; Stimpy, Rocko, Jenny and GIR. Often a mini-game or bonus level has to be completed before you can collect it.
|SpongeBob SquarePants||SpongeBob SquarePants|
|Patrick Star||SpongeBob SquarePants|
|Sandy Cheeks||SpongeBob SquarePants|
|Danny Phantom||Danny Phantom|
|Tucker Foley||Danny Phantom|
|Sam Manson||Danny Phantom|
|Timmy Turner||The Fairly OddParents|
|Cosmo||The Fairly OddParents|
|Vicky||The Fairly OddParents|
|Jimmy Neutron||The Adventures of Jimmy Neutron: Boy Genius|
|Goddard||The Adventures of Jimmy Neutron: Boy Genius|
|Carl Wheezer||The Adventures of Jimmy Neutron: Boy Genius|
|Tak||Tak and the Power of Juju|
|Jibolba||Tak and the Power of Juju|
|Lok||Tak and the Power of Juju|
|Ren Höek||The Ren & Stimpy Show|
|Stimpy Cat||The Ren & Stimpy Show|
|Dib Membrane||Invader Zim|
|Jenny (XJ-9)||My Life as a Teenage Robot|
|Brad Carbunkle||My Life as a Teenage Robot|
|El Tigre||El Tigre: The Adventures of Manny Rivera|
|Frida Suarez||El Tigre: The Adventures of Manny Rivera|
|Aang||Avatar: The Last Airbender|
|Katara||Avatar: The Last Airbender|
|Sokka||Avatar: The Last Airbender|
|Angelica||Rugrats (Console) / All Grown Up! (GBA)|
|Tommy Pickles||Rugrats (DS) / All Grown Up! (Console & DS)|
|Chuckie Finster||All Grown Up!|
|Mrs. X||The X's|
|Tuesday X||The X's|
|Truman X||The X's|
|Rocko Wallaby||Rocko's Modern Life|
|Spunky||Rocko's Modern Life|
|Daggett Beaver||The Angry Beavers|
|Norbert Beaver||The Angry Beavers|
|Otto Rocket||Rocket Power|
|Twister Rodriguez||Rocket Power|
|Krumm||Aaahh!!! Real Monsters|
|The Gromble||Aaahh!!! Real Monsters|
|Ginger Foutley||As Told By Ginger|
|Dodie Bishop||As Told By Ginger|
|Helga G. Pataki||Hey, Arnold!|
|Donnie Thornberry||The Wild Thornberrys|
|Darwin Thornberry||The Wild Thornberrys|
|Otis||Back at the Barnyard|
|Pip||Back at the Barnyard|
There are three bonus levels in the game. In the first one you play as SpongeBob. You have to slide down on your tongue through the sewer without hitting any obstacle. You can however bash into enemies to destroy them. The second minigame features Tak who has to reach his way to the exit while climbing up walls, evading spikes etc. The third minigame has Danny who turns invisible and has to activate generators within the time limit to go to the next room. He has to blast away blocks with his ghost powers for this.
- This marks Professor Calamitous second appearance as the main antagonist of the game.
- All four of the Nicktoons Unite! characters appear as playables.
- In the console version you only visit Bikini Bottom, Amity Park, Fairy World, and Calamitous' Lair while in the handheld version you visit Bikini Bottom, Amity Park, the Ghost Zone (GBA exclusive), Fairy World, Pupununu Village and Retroville.
- Plankton and the Mawgu both make a cameo appearance at the Biggest Genius game show as other competitors.