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 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 afterwards.
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 an 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 have 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 which 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 heroes faces are carved to honor them.
Timmy Turner (comes with Cosmo and Wanda, but you cannot specifically play them)
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.
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.
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 you manage to rapidly press the Melee button while near a Health/Missile crystal, it will spawn 4 shards instead of the normal 3.
This takes place after the episode, "Band Geeks," as evidenced by the fact that Mr. Krabs, SpongeBob, Sandy, Plankton, and Patrick had never seen a human before this episode, as referenced when Patrick said "These are some oddly looking fish." and SpongeBob saying "Maybe we're in one of those toxic waste dumps."
This takes place after the Jimmy Neutron and Fairly OddParents crossover, Jimmy Timmy Power Hour. As referenced by Jimmy and Timmy's knowledge of each other, as well as Jimmy's knowledge of Cosmo and Wanda. Also, Jimmy refers to Fairy World magic as "the power source from the game." Cindy also met Timmy in that episode, which is referenced at the end of Nicktoons Unite!.
It might also take place after Jimmy Timmy Power Hour 2: When Nerds Collide! because in that episode Mr. Crocker and Professor Calamitous had no interaction with each other after Professor Calamitous hit the "Welcome to Dimmsdale" sign when Mr. Crocker was putting up his birthday sign.
This takes place after Jimmy Neutron's Professor Calamitous, I Presume, and Danny Phantom's Bitter Reunions. As these we're the two episodes that Jimmy met Calamitous and Danny met Vlad.
This takes place after "Help Wanted" because SpongeBob knows Mr. Krabs.
This takes place after "Scaredy Pants" because SpongeBob knows the Flying Dutchman.
This also most likely takes place after "Shanghaied" because it seems like the Flying Duthman knows him more and is also afraid of him and SpongeBob seems familiar with the Duthman's ship.
This takes place after the Fairly OddParents' That Old Black Magic because Timmy has been to Fairy World.
This takes place after Fairly OddParents' Inspection Detection because Timmy knows Jorgen.
This takes place after the Oh Yeah Cartoons! short/Fairly OddParents' pilot, The Fairly OddParents! because Timmy knows Cosmo and Wanda.
This might takes place after Fairly OddParents' Abra-Catastrophe! because the exterior of Crocker's fortress looks similar to his fortress in that episode.
This takes place after Danny Phantom's One of a Kind because that is the episode where Danny met the Box Ghost and Skulker. (Skulker appeared in the episode below.)
This takes place after Danny Phantom's Prisoners of Love because that is the episode where Danny met Walker. He has also been to the Ghost Zone Prison before in that episode.
Because of that episode, this game is also after the episode Mystery Meat because that is the episode Danny met The Lunch Lady Ghost and she was in Prisoners of Love. Same with the episodes What you Want, Attack of the Killer Garage Sale, and Parental Bonding with the characters Desiree, Technus, and Princess Dorathea.
This takes place after "Frankendoodle" because that is the episode where SpongeBob met DoodleBob, which is used as an attack in Nicktoons Unite!.
Because of this episode, this game also takes place after "Bubblestand."
This game takes place after "Plankton!" because SpongeBob knows Karen.
This game takes place after The SpongeBob Movie: Sponge Out of Water because SpongeBob is not surprised when he sees humans and Plankton doesn't know what Teamwork is in that movie and in this game he works with a team.
This game takes place after the Danny Phantom episode, "Memory Blank" because Danny has his logo on his chest which he did not obtain until that episode.
Based off this game
This takes place after, and possibly shortly after, Nicktoons Unite! because SpongeBob, Danny, Timmy, Sandy, Cosmo, Wanda, Jimmy, and Patrick know each other. Also, Danny asks SpongeBob if he needs more of the spray that Jimmy used on SpongeBob at the Beginning of Nicktoons Unite!, and SpongeBob says that he is still fine. Also, Plankton's Giant Green Crab Suit was seen crashed on Volcano Island.
This takes place before Nicktoons: Attack of the Toybots, and SpongeBob SquarePants featuring Nicktoons: Globs of Doom. In Nicktoons: Attack of the Toybots, Danny, SpongeBob, Jimmy, Cosmo, Wanda, Timmy, and Patrick know each other and when Patrick, SpongeBob, and Tak get to Jimmy, SpongeBob says "look! It's Jimmy Neutron!" and Tak says "Jimmy who-tron?" and Patrick responds "Oh, he's a friend of ours. We go way back," referencing the past two games. In SpongeBob SquarePants featuring Nicktoons: Globs of Doom, Danny, Tak, Plankton, SpongeBob, Patrick, and the Wise Old Crab knew each other (except for the Wise Old Crab with Plankton and Tak and Tak with Plankton)
This takes place before Fairly Odd Baby, Fairly OddPet, and The Big Fairy Share Scare because neither Poof, Sparky, or Chloe are around with Timmy.