Tucker Foley, Squidward Tentacles, and Jimmy Neutron also appear, but only as support and are non-playable.
The game begins almost a year after Danny, Timmy, Jimmy, and SpongeBob had stopped the Evil Syndicate. When a far away island called Volcano Island is in danger, three crabs get together and perform a summoning to call The Nine to free their land from a creature called The Mawgu. When he overhears and attacks, he disrupts the summoning and all Nicktoons are scattered to parts of the island. However, two of the Nicktoons Danny Phantom and SpongeBob SquarePants have arrived at the Summoners Rock together. Then a crab Wizard known as The Wise Old Crab explains what's been happening and why they were summoned. Now, Danny and SpongeBob must travel together to reach their base camp area.
Upon learning the basics from the Wise Old Crab, SpongeBob and Danny run into Patrick bouncing on a diving board. Patrick joins them and the three continue on to a shipwreck on a cliff. After crossing the shipwreck, they find Danny's friend Tucker being attacked by seagulls. They eventually save him. Tucker questions Danny about the whole situation and the Wise Old Crab finally finds a safe spot to build their camp.
In the camp, the Wise Old Crab tells the whereabouts of the "Night Girl" (Sam) and the "Whiny Cephalopod" (Squidward). The heroes venture to a nearby lagoon where they find Sam fighting the sand monsters in the Fenton Peeler Suit. Sam mentions a weird noise on the other side of the lagoon and the heroes investigate to find a clarinet sticking out of the sand. SpongeBob knew right away that it was Squidward and pulls the clarinet freeing him. Squidward makes a sarcastic remark afterward.
Back at the camp, the Wise Old Crab tells the location of the "Three-Headed Boy" (Timmy and his Fairies) to be found in an armed fortress filled with exile crabs. After crossing the dense jungle, the heroes reach the fortress, being attacked by numerous crab soldiers as they infiltrate. They find Timmy, Cosmo, and Wanda leading a parade of crabs and it is revealed that they are actually being held captive. The heroes then head to the main gate to free Timmy and escape. After freeing him, Timmy finds a Jimmy Neutron communicator, however, it is lacking a battery so the heroes were unable to communicate with Jimmy.
Back at the camp, SpongeBob and Danny find a crab villager in desperate need of help. His village is being attacked by a giant sand monster called "The Great Carrapace." They then head to the village and defeat the sand monster. The Wise Old Crab awards them with a jewel which happens to be the communicator battery. They finally made contact with Jimmy Neutron (still in Retroville) and he tells them that the Mawgu is using a dimensional rift to harness energy from all of their homeworlds which would eventually lead to their destruction. Jimmy gives the heroes the blueprints to the Neutron Rip Zipper (a machine that will drain the Mawgu of its power). The heroes now must search the island for parts.
The Wise Old Crab tells the location of the last hero, the "Deep Sea Squirrel" (Sandy). They head out to ancient ruins to find Sandy in a scuffle with the rock monsters. After helping her out, Tucker informs the group that a Rip Zipper part is nearby. Sandy finds the part behind a crystal wall and breaks it along with SpongeBob with their karate skills. Sandy then questions them of what's going on. After Patrick's long story of him "jumping," Sam finally tells her that they must save the universe.
At the camp, the Wise Old Crab desperately tells the heroes that the queen of the Myrmecs has been kidnapped by the Florian tribe and being held captive at an oose mine. The heroes head out and free the queen from her captors. Jimmy also informs another Rip Zipper part is found nearby and the heroes collect it. Back at the camp, the Queen tells the heroes that the Florian tribe leader King Gorge build a dam to stop the water flowing through their village and now they're forced to drink the ooze, making them slaves to the Mawgu.
The heroes confront King Gorge. Sam begs him to stop but King Gorge refuses. As the heroes fight him, the Myrmecs start chipping away at the dam and it finally collapses. The water converts King Gorge back to his original self, awarding them with the final part of the Rip Zipper.
Now the heroes finally set out to the Mawgu's lair, the volcano. After reaching the summit, they confront the Mawgu and follow him to the dimensional rift above. The other heroes distract him while SpongeBob and Danny scale the debris floating through the rift. SpongeBob and Danny finally battle him and use the Rip Zipper to drain him of his power. After that, Tucker opens a portal that sucks the Mawgu and sealing him for good.
After the battle, Jimmy activates a portal for the heroes to go home. The Wise Old Crab (his true name Shelly) and the Myrmec Queen thank them for their help. After the heroes leave, the camera then zooms to a cliff where the hero's faces are carved to honor them.
Timmy Turner (comes with Cosmo and Wanda, but you cannot specifically play them)
All versions of this game have backwards compatibility.
The PS2 version can be played on old PS3 units.
The GameCube version can be played on various Wii units.
The GBA version can be played on all DS and DS Lite units.
The DS version can be played on all 3DS/2DS/DSI units.
If one looks closely, the robot from Nicktoons Unite! that had been used by Plankton can be seen in Level 1 as a junk in the background, only seen when you take the top path in the fork in the road.
Invader Zim is 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 was the first Nicktoons game to have a Japanese release.
In the UK, the cover art was different.
The PS2, GameCube versions have the same gameplay, while the GameBoy Advance and Nintendo DS versions each have their own gameplay style.
Timmy Turner has 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.
A Nicktoons parody of Mount Rushmore is shown during the final cutscene in the console version.
The concept art of this game revealed a few ideas that were scrapped 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.
If the player manages to rapidly press the Melee button while near a Health/Missile crystal, it will spawn four shards instead of the normal three.