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The opening intro for the game features Professor Calamitous on a game show called the Biggest Genius. Calamitous states that by feeding fairies Krabby Patties, they can emit a magical gas that, combined with Ghost energy, can be used as a form of fuel for his army of "Toybots."
As the opening credits are shown, the game itself opens with Patrick Star and SpongeBob SquarePants delivering a truckload of several million Krabby Patties to a Krabby Patty processing and Toybots factory. Upon arriving at the factory, a robot sucks up all the Krabby Patties, and Patrick, unintentionally, in the process. Determined to save his best friend and the Krabby Patties, SpongeBob disguises himself as a FactoryBot and manage to infiltrate the factory.
After finding his way through the factory, SpongeBob finds Patrick vacuum-packed like a toy in the factory warehouse. After freeing him, they meet Tak , of the Pupununu People, who was hiding there after being abducted and scanned by the Toybots. The trio then make their way through the main EvilToyCo factory where they discover Timmy Turner and Jimmy Neutron imprisoned in Irken-themed rooms, both also claim to have been abducted and scanned. After going through the first zone of the factory, they meet the Chad-Bot, a robot who reveals himself to be Professor Calamitous's helper, but is in reality, unhappy with him. The heroes ask if he could contact Danny Phantom to which Chad-Bot accept only if they find action figures called "Master Models" for his collection.
After collecting a few Master Models in the second zone of the factory, Jimmy contacts Danny Phantom, who says that Calamitous' invading toy army took over his house to use the energy coming from the Ghost Zone and its surrounding by big tin robots that looks like him and Sam. Jimmy tells Danny and Sam to meet him and the other heroes at the Amity Park EvilToyCo outlet. When they get there, they discover that Jimmy made Mech-Suits in order to fight the big tin Robots. After stopping the Toybots invasion on Amity Park and defeating a Giant Evil Toy Jimmy Head, they head back in Chad-Bot's basement.
There, Chad-Bot tells them that they must stop the Saucer-Men toys to capture any more heroes, the group travel through the factory's third zone and collect others Master Models along the way. After destroying the Saucer-Men toys, the heroes head to Fairy World and discover a device called the "Fairly Harvester" which is used to lure and capture fairies. The group follows the machine's pipes where they find and freed Jorgen Von Strangle, the latter thanks the heroes and destroys the Fairly Harvester.
After cutting Calamitous from its supply of Ghost Energy and Fairies, The heroes head to the last zone of the factory where they fight their way through the Professor's lair using their Mech-Suits, The heroes arrive on the Biggest Genius set and find out that 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. Chad-Bot thanks the heroes for helping him and the game ends with Chad-Bot cutting Calamitous' mustache off with an electric shaver.
Game Boy Advance
This version opens with Professor Calamitous talking about his plan to take over the world with toybots and how he kidnapped SpongeBob, Timmy, Jimmy, Danny, and Tak.
"I can turn into a skyscraper!"
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The gameplay includes playing as two Nicktoons in some levels and plotting an operational Mech suit in others. Players journey through Bikini Bottom, Amity Park, Fairy World and Calamitous' Lair, as well as the Toybot Factory, which is divided into multiple segments.
Nintendo DS version
The Nintendo DS version is a more simplified 2D platformer that relies heavily on the touch screen where characters are commanded to move by swiping them on the direction the player wants them to go while also interacting with the environment. Players journey through Bikini Bottom, Amity Park, Fairy World, Pupununu Village, Retroville and Evil Toy Company.
Game Boy Advance version
The Game Boy Advance version of the game is a 2D side-scroller platformer.
James Isaac "Jimmy" Neutron
Timmy Turner (with Cosmo and Wanda)
Patrick Star (Console/Nintendo DS versions)
Sam Manson (Console version)
Zim (Nintendo DS version)
Stimpy J. Cat (Console version)
Rocko Wallaby (Console version)
Jenny Wakeman/XJ-9 (Console/Nintendo DS versions)
GIR (Console/Nintendo DS version)
El Tigre (Nintendo DS version)
Mr. Blik (Nintendo DS version)
Mr. Huggles (Console version, can be unlocked by entering a cheat code)
Exo-Huggles 9000 (Console version, can also be unlocked by entering a cheat code)
SpongeGar aka Prehistoric SpongeBob (unlockable costume in console version) (can be unlocked by entering a cheat code in the Nintendo DS version)
Evil Danny (unlockable costume in console version) (can be unlocked by entering a cheat code in the Nintendo DS version)
They are three unused SpongeBob, Danny Phantom, and Timmy Turners bonus levels in the game alongside their respective tracks. A few Master Models went unused in the console version, most of them are characters from KaBlam! and Action League Now!.
Two concept art showcase a scrapped character called "Rusty Beard" and his ship that would've been used to navigate through Nickelodeon universes. It's possible that they may come from an earlier version of the game storyline. Other concept art also show a few scrapped ideas such as different designs for the Mech-Suits or SpongeBob, Patrick and Danny Phantom standing in front of the entrance of the EvilToyCo factory, something that never happen in-game.
PlayStation 2 version
Nintendo DS version
This game reveals that fairies like Krabby Patties.
This was the first Nicktoons game released for the Wii.
This was the first Nicktoons game not to be released for the GameCube.
This is the only Nicktoons game where the player can pick their own characters.
Since the first level takes place underwater, in the console version of the game Tak should not have been able to breathe in the cutscene because he never met Jimmy, who had in Nicktoons Unite! invented gum that allowed the other Nicktoons to breathe underwater.
This error is not present in the handheld versions, as Tak had met Jimmy beforehand in the Nintendo DS version, while in the Game Boy Advance version, the first level doesn't take place underwater.
In the Game Boy Advance version, Professor Calamitous is designed in the same style as The Fairly OddParents.
Patrick is seen in the Game Boy Advance cover of the game depsite being not playable.
Despite being playable characters in the home console version, Rocko, Stimpy, GIR, and Jenny are completely absent in every cutscene.
Same goes for the Nintendo DS version, where the latter two, Invader Zim, Mr. Blik, & El Tigre are absent too.
In the Nintendo DS version, Danny says "Woah, so this is really Fairly World" but however he went to Fairly World in Nicktoons Unite!.