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 vacuum-packed like a toy. After freeing Patrick, 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 (which is almost destroyed) 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 was in a frozen state on till Patrick bumped into him thanks to Jimmy), who destroys the fairly 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 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.
This takes place after the episode "Band Geeks," as evidenced by the fact that Mr. Krabs, SpongeBob, Sandy, Plankton, and Patrick had never seen a human before this episode, as referenced when Patrick said "These are some oddly looking fish." and SpongeBob saying "Maybe we're in one of those toxic waste dumps."
This takes place after the Jimmy Neutron and Fairly OddParents crossover, Jimmy Timmy Power Hour. As referenced by Jimmy and Timmy's knowledge of each other. As well as Jimmy's knowledge of Cosmo and Wanda. Also, Jimmy refers to Fairy World magic as "the power source from the game." Cindy also met Timmy in that episode, which is referenced at the end of Nicktoons Unite!.
It might also take place after Jimmy Timmy Power Hour 2: When Nerds Collide! because in that episode Mr. Crocker and Professor Calamitous had no interaction with each other after Professor Calamitous hit the "Welcome to Dimmsdale" sign when Mr. Crocker was putting up his birthday sign.
This takes place after Jimmy Neutron's Professor Calamitous, I Presume, and Danny Phantom's Bitter Reunions. As these we're the two episodes that Jimmy met Calamitous and Danny met Vlad.
This takes place after "Help Wanted" because SpongeBob knows Mr. Krabs.
This takes place after "Scaredy Pants" because SpongeBob knows the Flying Dutchman.
This also most likely takes place after "Shanghaied" because it seems like the Flying Dutchman knows him more and is also afraid of him and SpongeBob seems familiar with the Dutchman's ship.
This takes place after the Fairly OddParents' That Old Black Magic because Timmy has been to Fairy World.
This takes place after Fairly OddParents' Inspection Detection because Timmy knows Jorgen.
This takes place after the Oh Yeah Cartoons! short/Fairly OddParents' pilot, The Fairly OddParents! because Timmy knows Cosmo and Wanda.
This might takes place after Fairly OddParents' Abra-Catastrophe! because the exterior of Crocker's fortress looks similar to his fortress in that episode.
This takes place after Danny Phantom's One of a Kind because that is the episode where Danny met the Box Ghost and Skulker. (Skulker appeared in the episode below.)
This takes place after Danny Phantom's Prisoners of Love because that is the episode where Danny met Walker. He has also been to the Ghost Zone Prison before in that episode.
Because of that episode, this game is also after the episode Mystery Meat because that is the episode Danny met The Lunch Lady Ghost and she was in Prisoners of Love. Same with the episodes What you Want, Attack of the Killer Garage Sale, and Parental Bonding with the characters Desiree, Technus, and Princess Dorathea.
This takes place after "Frankendoodle" because that is the episode where SpongeBob met DoodleBob, which is used as an attack in Nicktoons Unite!.
Because of this, the game also takes place after "Bubblestand."
This game takes place after "Plankton!" because SpongeBob knows Karen.
This game takes place after The SpongeBob Movie: Sponge Out of Water because SpongeBob is not surprised when he sees humans and Plankton doesn't know what Teamwork is in that movie and in this game he works with a team.
This game takes place after the Danny Phantom episode, "Memory Blank" because Danny has his logo on his chest which he did not obtain until that episode.
Based off this game
This takes place after Nicktoons Unite! and Nicktoons: Battle for Volcano Island because SpongeBob, Danny, Timmy, Sam, Cosmo, Wanda, Jimmy, Patrick, and Professor Calamitous know each other. In addition, Calamitous is aware of fairy magic and Krabby Patties as he uses the Krabby Patties to make the fairies magically fart to allow his Toybots to be alive.
This takes place before SpongeBob SquarePants featuring Nicktoons: Globs of Doom. In SpongeBob SquarePants featuring Nicktoons: Globs of Doom, Danny, Tak, Plankton, SpongeBob, Patrick, and the Wise Old Crab knew each other (except for the Wise Old Crab with Plankton and Tak and Tak with Plankton)
This takes place before both Fairly Odd Baby and Fairly OddPet because both Poof and Sparky are not around with Timmy.
Since the first level takes place underwater, in the console version of the game Tak should not have been able to breathe in the cut scene because he never met Jimmy, who had in Nicktoons Unite! invented gum that allowed the other Nicktoons to breathe under water. Although, it is possible that his magic allows him to breathe.
This error isn't present in the DS or GBA versions of this game, as Tak had met Jimmy beforehand in the DS version and the first level didn't take place underwater in the GBA version.