One morning, when SpongeBob SquarePants goes out of his house, he sees that Plankton has taken over Bikini Bottom and used multiple tank-like vacuums to suck away all of the town's civilians. He sees Goddard coming out through a portal and receives a message from Jimmy Neutron. He follows Goddard through the portal to Jimmy's lab and meets Jimmy Neutron, Danny Phantom, and Timmy Turner. Since SpongeBob is an aquatic being in need of water, Jimmy uses one of his few non-backfiring inventions to coat SpongeBob in a coat of self-regenerating moisture. Jimmy tells his inter-dimensional guests about his new invention, The Universe Portal Machine. As he says, it allows people to travel to other worlds. But Prof. Calamitous has been spying on him, stole his idea and created his own Portal Machine. With it, he brought Plankton, Vlad Plasmius, and Denzel Crocker to his dimension. They formed a Syndicate and proceed to steal energy from all the worlds. Since our heroes do not know where Calamitous lair is, they start with saving all of their worlds first.
Danny suggests that they go to his world first, so Jimmy uses the portal machine to take them to Casper High in Amity Park. However, much to their surprise they end up in the throne room of Vlad's new castle, which he built over Casper High. Vlad reveals that he is using his personal ghost-portal to siphon ghost energy from the Ghost Zone to help further the Syndicate's ultimate plan. Also, as a precaution, Vlad had captured (unknown to the rest of the good guys) Danny's parents. As usual, Vlad tries to win Danny over to his side, but Danny rebuffs the offer as usual. Confident, Vlad knocks them unconscious and imprisons in the Ghost Zone Prison now under his control. Befriending the imprisoned Box Ghost, the Nicktoons escape their holding area and proceed onwards with Danny phasing through the walls and deactivating the machines that keep physical beings from escaping. However, at the exit, the meet the Warden of the Prison, Walker, who is not too happy with their prison break. Knocking Walker out, Danny leads the heroes to the ghost-portal leading to the basement of Fenton Works, where he quickly lies that he has no relation to the Fentons and that they are the experts in Ghost Hunting. They exit Fenton Works and encounter Danny's friends, Sam and Tucker, who tell them some of the people in Amity Park have been possessed by the ghosts released from Vlad's portal.