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The game begins in Bikini Bottom where SpongeBob is about to visit Patrick. However, he hears an announcement from Plankton that he will rule Bikini Bottom. When the townspeople refuse to allow that, he orders two tanks to capture them. SpongeBob hides and is worried that Plankton will get a chance to shut down the Krusty Krab once he gets the Krabby Patty formula.
Just then, Goddard came from a portal and Jimmy informs SpongeBob that Plankton has joined forces with villains from other worlds and with their help, he has taken over Bikini Bottom. He tells SpongeBob to join with him so that they can defeat the villains
Upon going to Jimmy's lab, he is greeted by Danny Phantom and Timmy Turner, respectively. Jimmy lectures the three that his archenemy, Professor Calamitous has stolen his ideas for a portal machine and uses it to build one of his own. With it, he has allied with Crocker, Vlad Plasmius, and Plankton, and they formed a syndicate. They build numerous devices for them to suck up energy from their own worlds.

After that, the heroes go to Amity Park. However, they were confronted by Vlad in his castle. He reveals that he has Danny's parents hostage and he will let them go if Danny joins with him, the offer that he refuses. Vlad stuns them with his energy blasts, saying that he will send them in the Ghost Zone prison.
Inside, they were confronted by Walker. After escaping, they fixed the messed in the town from ghosts and proceed to go to Vlad's castle to disable the generators that powered up Vlad's portal. Then, they confront Vlad and they defeat him. However, he escapes from them.
The four heroes go to Bikini Bottom where they meet Sandy and follow her to the Krusty Krab where she tells them about Plankton and the Jellyfish Factory. Fortunately, she sends a secret agent there. By the time they got to Jellyfish Fields, Patrick is revealed to be the secret agent and is captured by Plankton. They rescue him in the factory and confront Plankton in the rooftop of the Chum Bucket where he tries to get the Krabby Patty formula from Krabs. Plankton fights the four with a crab mech and is defeated. However, he escapes. The four heroes have discovered that the villains are extracting energy for a doomsday device.
They go to Dimmsdale in Crocker's fortress where they re-activate the prisms in order to get to Fairy World. Afterwards, they meet Jorgen Von Strangle who explains to them that Crocker is extracting magic from the Big Wand. After freeing the fairies, the heroes confront Crocker in the Big Wand and they beat him.
The heroes learn that each them they beat their respective enemies, they always escape. SpongeBob assumes that it is part of their plot.
By the time they go back to Jimmy's lab, Calamitous makes an announcement of the doomsday device. Just then, Goddard begins to scratch, leading Jimmy to realize that Calamitous is spying on him through a flea bot inside Goddard. The four heroes go inside Goddard where they defeated the flea bot and use it to find where Calamitous and the other villains are.
When they got to the warehouse, the villains are in a wheel-like device and a shield for each of them for protection. After defeating them, Calamitous remarks that the doomsday device is still on and it can't be stopped. However, SpongeBob plugs the device off and Calamitous says that he didn't finish the backup supply.
Timmy, Danny, and SpongeBob go back to their worlds and Jimmy shouts at Cindy "Get out of my lab!"

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