The plot goes around that the universe is in trouble. In every universe there are Dark Toons send by the villains.
Chapter 1: Tutorial
SpongeBob was having a normal day in Bikini Bottom working in the Krusty Krab. Suddenly a huge Plankton-like robot attacked. It captured SpongeBob, Patick, Sandy, Squidward and Mr. Krabs. Only SpongeBob and Patrick managed to break free, the robot opened a door and all Dark Toons stepped out and fought the two until Jimmy Neutron summoned them to Volcano Island.
They meet the Wise Old Krab who tells them that in every dimension the villains have send the Dark Toons. Others who were on the island were Jimmy, Timmy, Danny, Tak, Zim, Aang, El Tigre and Dudley. The whole team completed a tutorial level on Volcano Island.
Chapter 2: Master of Juju
The heroes went to Pupununu Village where they go through several areas of the dimension. They underway in the jungle see Lok who was fighting a Swamp Monster who has captured Sam but he couldn't do it alone. He joined the team and they headed further to the village where the Swamp Monster was attacking the buildings. The team fights him and free Sam who says that in the temple there is a huge monster. They all head to the temple where they encounter El Mal Verde and fight it. After they have defeated it they find U.B. caged behind it and they free him. After this they also find the keyhole of the dimension which is on the middle of the temple's floor.