It was followed by Nicktoons: Attack of the Toybots a year later.
On Volcano Island, a couple of crabs, led by The Wise Old Crab, are enacting a ritual to send 9 heroes there to save their island. But the Mawgu, an evil being, brings the ritual to a halt, scattering the heroes. Danny Phantom and SpongeBob SquarePants fall from the sky and end up with the Wise Old Crab, and he explains why they were dropped here: The Mawgu was an ancient enemy who escaped his prison, and seeks vengeance, using a toxic ooze which corrupts everything it touches, but the prophecies say that "The Chosen Ones" will save them. The Crab trains them and tells the heroes to follow him so that he can direct them to camp. The heroes stop various enemies, and then find Patrick. They then go Shipwreck Cliff and rescue Tucker from repeatedly regurgitating giant seagulls. They then find camp, and are given the mission to find the "Night Girl (Sam Manson)" and the "Whiny Cephalopod (Squidward Tentacles)", and they are found.
Timmy Turner is then found at Fort Crabclaw with a Jimmy Neutron communicator which fell from the sky. However, the machine has no batteries. The heroes are then sent to destroy The Great Carapace, a giant sand monster with a wooden shell. They destroy the shell and push the monster into a waterfall by using catapults and coconuts. They are then rewarded with a jewel, which is the battery for the communicator. They talk to Jimmy using the communicator, and Jimmy explains that Mawgu is using a Rip in Time and Space to steal energy from all the worlds and keep it all for himself, and if he succeeds their worlds will be destroyed. Then Jimmy sends Tucker plans for the Neutronic Rip- Zipper, a device that recovers all the energy Mawgu stole and closes the Rip. The parts they need for the device are scattered across the Island. Then the wise old crab says that he knows where the last hero is, the deep sea squirrel (Sandy Cheeks) after they climb a pyramid, they find Sandy fighting Monsters. After the heroes help her they find the first part for the rip-zipper behind a crystal wall. After the Nicktoons gain all three Rip-Zipper items, they go in the Volcano, and find The Mawgu, whom transports them between Time and Space. The Nicktoons then succeed in defeating Mawgu, imprisoning him within the Rip, and closing it.
The heroes are praised for the save of the island and Jimmy is able to activate a portal to send them home. It shows at the end, that the heroes heads' are carved on the side of a mountain.
These are the characters the player can take control of.
- Danny Phantom (Ghost Boy)
- SpongeBob SquarePants (Absorbent Yellow One)
- Timmy Turner (Three-Headed Boy)
- Patrick Star (console & GBA exclusive)
- Sam Manson (Night Girl) (console exclusive)
- Sandy Cheeks (Deep Sea Squirrel) (console exclusive)
- Tucker Foley (console and DS exclusive)
- Squidward Tentacles (The Whiny Cephalopod) (console exclusive)
- Jimmy Neutron
- Mawgu: The main antagonist of the game.
- Great Carapace: A giant sand monster with a giant wooden shell on its back. (console exclusive)
- Mad King Gorge: A king of another clan on the island being controlled by Mawgu's ooze. (console exclusive)
- Gorge's Sergeant: The sergeant of Mad King Gorge who is fought as mini-boss. (console exclusive)
Main Article: Volcano Island
- Summoners Rock
- Shipwreck Cliff
- Camp Castaway (Main Hub)
- Calamity Cove
- Fort Crabclaw
- The Great Carrapace
- Crystal Ruins
- Fetid Forest
- Dry Canyon Dam
- Ancients Peek
- Summit Storm
- Bird Nest
- Sand Monster
- Giant Sand Monster
- Sand Ooze Spout
- Mermec Bug
- Crab Soldier
- Crab Hut
- The Great Carrapace (Boss)
- Shrub Monster
- Purple Shrub Monster
- Shrub Ooze Spout
- Crystal Scorpion
- Florian Tribeman
- Florian Sargent
- King Gorge (Boss)
- Rock Monster
- Guardian Rock Monster
- Rock Ooze Spout
- Mawgu (Final Boss)
In the game, there are many interactive items the player can use to advance in the game, whether or not it's to advance in the level, or the whole game.
Nuts are some Coconuts and exotic nuts the player can pick up and throw at obstacles to break them. In the earlier levels, the nuts are small, round, and have a classic, bomb-like white string at the top of them, but after Fort Crabclaw, the nuts become giant, oval-shaped and are cracked.
Levers are used in the game to activate a crane, drop a pipe, etc. to advance in a level. They are rarely found in the game.
There are many pickups in the game to restore health and charge ranged weapons. Blue Energy restores health, while Orange Energy gives you one shot. The player can carry up to 5 shots.
Costume Pickups are small items the player must collect to "create" a costume the player can use in-game. SpongeBob SquarePants' items are clams, his costume is a pirate. Danny Phantom's items are cogs, his costume is the Fenton Suit. Patrick Star's items are tusks, they are hard to find, as you must punch a specific shrub, causing a warthog to run around and drop tusks. Patrick Star's costume is an island native. Sam Manson's items are "mysterious" tikis, her costume is the prom dress. Timmy Turner's items are alien fruit, his costume is Crash Nebula. Sandy Cheeks' items are feathers, the way to find them is quite similar to tusks, you must punch the trees that shake and a bird will fly away dropping feathers. Her costume is a cheerleader.
Salvage Items are special items used to unlock bonus levels and extras. Salvage Items for Danny Phantom, Timmy Turner, SpongeBob SquarePants, Sandy Cheeks, Sam Manson, and Patrick Star unlock Bonus Levels, such as "Ghost Zone Zoomin'" and "Goofy Goober Rush." There are Salvage Items for the NPCs. Salvage Items for Tucker Foley and Squidward Tentacles unlock the Movie Theater and the Art Gallery.
- David Kaufman - Danny Phantom
- Tom Kenny - SpongeBob SquarePants
- Bill Fagerbakke - Patrick Star
- Rickey D'Shon Collins - Tucker Foley
- Grey DeLisle - Sam Manson
- Rodger Bumpass - Squidward Tentacles
- Tara Strong - Timmy Turner
- Daran Norris - Cosmo
- Susan Blakeslee - Wanda
- Debi Derryberry - Jimmy Neutron
- Carolyn Lawrence - Sandy Cheeks
- Bill Farmer - The Wise Old Crab, King Gorge, Plant Guard, Crab Refugee 4
- Fred Tatasciore - The Mawgu, Crab Sarge, Gorge's Sergeant
- Saffron Henderson - The Queen of the Myrmecs, Crab Follower 1, Crab Refugee 1, Crab Refugee 3
- Amber Hood - Little Crab
- Nolan North - Crab Soldier 1, Crab Soldier 2, Crab Refugee 2
- James Peak - Crab Follower 2, Crab Follower 3, Insect Carrier
- SpongeBob and Danny are the main characters of the game, being featured in every story mode level.
- If you look closely, the robot from Nicktoons Unite! that had been used by Plankton can be seen in Level 1 as a junk in the background.
- Invader Zim has been referenced twice in this game. In Fort Crabclaw, Zim's spaceship is seen resting on a tree trunk and in Summit Storm, Zim's house is seen in the background. This is likely a foreshadow for the sequal games as GIR was playable in Nicktoons: Attack of the Toybots and both Zim and Dib were playable in Nicktoons: Globs of Doom.
- Timmy Turner is the only character to have the least playable roles in the console version. He is only playable in Crystal Ruins and his bonus level.
- Some of the Salvage Items were taken from the cartoons while others reflect on the characters' personalities and traits.
- Tucker is the only character to have two of his Salvage Items located in the same level.
- The concept art of this game revealed a few ideas that were scraped from the final release. One specific artwork showed SpongeBob and Danny fighting a Florian robot in the Fetid Forest, which meant that the Florian robots seen in the background were originally going to be made as enemies.
- This is the first game in which you can play as characters who aren't from the main character in their show.