In the console version, all four characters are on-screen at the same time. The player has the option to switch between them, with the non-selected characters being automatically controlled. The console version also offers multiplayer, where up to four players can control and switch between the characters as well. Each character has several abilities for specific situations, such as SpongeBob's pillar-destroying Bubble Bombs, Danny's glass-breaking Ghostly Wail, Timmy's water-freezing Freeze Glove, and Jimmy's long-range Neutron Flare. Jimmy's dog Goddard can be found in all four worlds, including the level that takes place inside himself, to upgrade the player's weapons and abilities.
The Nintendo DS version is a 3D platformer where the player controls one of the four characters at a time, which can be selected at any moment via the touchscreen. The Game Boy Advance version is a 2D platformer in which the player must alternate between the two characters given at the beginning of the level in order to progress. It uses pre-rendered 3D sprites based on the models of the Nintendo DS version.