While Spongebob's group is setting up a plan to bring back the other lougers who abandoned them since Spyro and Sparx left to be with Kairi, Ignitus informs them that the Villain Leage and the Syndicate of Darkness is plotting an invasion in the Nentendo Universe including the Pokemon World. Unknown to everyone that the threat is the work of a powerful new non-darkspawn known as Tabuu, the master of Subspace. So Spongebob's group while bringing Kairi along encounter many video game characters of the Nentindo Universe like Mario, Kirby, Link, Donkey Kong, Pit and some familier faces like Sonic the Hedgehog.