- Four of Nickelodeon's most popular cartoon characters join forces to prevent their archnemeses from achieving global domination.
- SpongeBob goes outside to discover that Plankton is harboring the citizens of Bikini Bottom by order of a new Syndicate. A portal opens up and Goddard, Jimmy's Dog appears out of it. He displays a webcast of Jimmy Neutron requesting SpongeBob to follow Goddard into the portal to discuss the situation. The portal leads him to Jimmy's Lab where Timmy, and Danny are also waiting. Jimmy informs them that a Syndicate has been formed by Plankton, Mr. Crocker, Vlad, and Professor Calamitous, in order to obtain energy sources from each of their worlds. They enter the transporter to Amity Park, only to transport them to Vlad's Castle. Vlad makes an offer to Danny that if he joins his side, he will release his captured parents. Danny refuses, causing Vlad to put them unconscious and send them to The Ghost Zone Prison. They awake to find out that old enemy Walker has taken over the prison and intends to keep them there. Our heroes navigate through the prison however and defeat Walker in the prison yard. Danny leads them to a Ghost Portal that leads them to his parent's They arrive in Amity Park to find that most of the denizens have become possessed by ghosts. After ridding the Park of ghosts, they infiltrate Vlad's Castle.
Our heroes storm the castle and destroy the generators, and enter the throne room of Vlad. They learn from Vlad that they have enough energy to construct a device, until Danny uses his ghost powers to posses Phil father and defeat Vlad. Vlad escapes and our heroes use a portal to travel to Bikini Bottom. They are circled by guards until Sandy steps in and saves them. Sandy leads them through the ruins of Bikini Bottom and takes them to an enclosed Krusty Krab. She informs them that Plankton has taken over Bikini Bottom and has captured Mr. Krab said and several other resistors. She sends them to Jellyfish Fields to destroy the harvesters Plankton is using to harbor the Jellyfish's Sting energy. Our heroes go in to make contact with Sany's entrusted 'Agent Star.' Who turns out to be Spongebob's friend Patrick.
Patrick is harvested by one of the Jellyfish Harvesters, and is taken away. Our heroes arrive to the Ghost Ship of The Flying Dutchman, wherein they find a crew for The Flying Dutchman. They uncover an entrance to Plankton's Fortress, where they release Jellyfish from the factory vents. They free Patrick from a glass jar where they arrive to the roof where Plankton is interrogating Mr. Krab said for his formula. Plankton attacks them using a robot crab, only to be defeated by our heroes and smashed by Patrick falling from the sky. Plankton reveals that they are harnessing Dimsdale's energy for a doomsday machine, and he takes off.
They make their way to Crocker's compound where Fairy World's magic is being extracted. After shutting down the machines, they teleport to Fairy Town using a prism in the fortress. Once in Fairy World, they discover that Crocker is extracting the magic using the Big Wand Tower. Jorgen VonStrangle arrives and criticizes Cosmo and Wanda for bringing "puny children" as opposed to actual heroes. But he is then convinced of their worth and demands they free the captured fairies. The Fairies are freed and Jorgen takes them to a rout that leads to the Big Wand Tower. Crocker unveils that he is powerful thanks to the Fairy's Magic, and that the syndicate is now capable of worldly destruction. A showdown occurs and our heroes shut down Crocker's machine. With the Fairy's Magic restored, Crocker vows that their Doomsday Machine will triumph.
Our heroes return to Jimmy's Lab and find Cindy has arrived at the lab. Angry over how Jimmy has ruined everything. Professor Calamatious appears on Jimmy's Computer and states that all the world must obey him. SpongeBob points out that Goddard "needs a bath," leaving Jimmy to realize that Calamatious has been leaking information through a Fleabot on Goddard. So our heroes shrink down to size and voyage throughout hr inside of Goddard to find the parasitic nanobot and retrieve whereabouts on Calamatious's lab using a signal the nanobot is transmitting.
After defeating the flea, they find out that their lair is underneath an abandoned warehouse, and they ride the hover car over to finish them off. They enter the lair and to find the villains in a Ferris wheel like machine that will prevent them from suffering in the detonation. As the Doomsday Machine is set to detonate Retroville in five minutes. The capsule is destroyed only to find that the Doomsday Machine is counting down to thirty seconds. But the device shuts off after SpongeBob removes the plugs. They return to the lab where Jimmy gives the others some going away gifts, and a recaller in case something else happens. SpongeBob, Danny, and Timmy return to their respective homes and Jimmy orders Cindy out of his lab.
The End
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