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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 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, and eventually finds his way into the factory.
After finding his way through the factory, SpongeBob finds Patrick's vacuum-packed like a toy. After freeing him, they meet Tak, of the Pupununu People, who claims to have been abducted and scanned. They later find Timmy Turner and Jimmy Neutron, who also claim to have been abducted and scanned. They meet the Chad-Bot, a robot who is the Professor's 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 contacts Danny, who says that Calamitous' invading toy army took over his house to use the energy coming from the Ghost Zone and its surrounding with robots, that looks like him and Sam. So Jimmy tells Danny and Sam to meet him and the other Nicktoons at the Amity Park Evil Toy Co. outlet and when they get there they see that 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, collect 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 destroys the fairly harvester, and then get back into the Mech-Suits to the Professor's lair.
They get to where the opening intro 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 an electric shaver.
Game Boy Advance
This version opens with Professor Calamitous taking 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, Pupununu Village (handheld version only), Retroville (handheld version only), and Calamitous' Lair (console version only), as well as the Toybot Factory, which is divided into multiple segments.
The 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,
Game Boy Advance
The GBA version of the game is a 2D side-scroller platformer.
James Isaac "Jimmy" Neutron
Timmy Turner (with Cosmo and Wanda)
Patrick Star (Console/DS versions)
Sam Manson (Console version)
Zim (DS version)
Stimpy J. Cat (Console version)
Rocko Wallaby (Console version)
Jenny Wakeman/XJ-9 (Console/DS versions)
GIR (Console/DS version)
El Tigre (DS version)
Mr. Blik (DS version)
Mr. Huggles (can be unlocked by entering a cheat code)
Exo-Huggles 9000 (can also be unlocked by entering a cheat code)
SpongeGar aka Prehistoric SpongeBob (unlockable costume) (in DS version can be unlocked by entering a cheat code)
Evil Danny (unlockable costume) (in DS version can be unlocked by entering a cheat code)
Plant Girl Sam (unlockable costume)
Secret Agent Jimmy (unlockable costume)
Cowboy Timmy (unlockable costume)
Barnacle Boy Patrick (unlockable costume)
Chicken Suit Tak (unlockable costume)
Pilgrim Rocko (unlockable costume)
Flame-colored Jenny (unlockable costume)
Dog Disguise GIR (unlockable costume)
Kited Yaksman Stimpy (unlockable costume)
Professor Calamitous (the main antagonist)
Jorgen Von Strangle (Console version)
Chad-bot (Console version)
Fairies (Console version)
The Mawgu (cameo)
Vlad Plasmius (mentioned)
Denzel Quincy Crocker (mentioned in the DS version)
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 DS or GBA versions of this game, as Tak had met Jimmy beforehand in the DS version and the first level did not take place underwater in the GBA version.
Professor Calamitous from The Adventures of Jimmy Neutron: Boy Genius in the GBA version is designed as a character in The Fairly OddParents style.
Despite being playable characters in the home console version, Rocko, Stimpy, GIR, and Jenny were completely absent in every cutscene.