One morning, when SpongeBob leaves his house, he sees that Plankton has taken over Bikini Bottom and used multiple tank-like vacuums to suck up some of the town's citizens. He sees Goddard coming out through a portal and receives a message from Jimmy. He follows Goddard through the portal to Jimmy's lab and meets Jimmy Neutron, Danny Fenton, and Timmy Turner. Jimmy tells his inter-dimensional guests about his new invention, the Universe Portal Machine. As he says, it allows people to travel to other worlds, but Prof. Calamitous has been spying on him, stole his idea, and created his own Portal Machine. With it, he brought Plankton, Vlad Plasmius, and Mr. Crocker to his dimension. They formed a syndicate and proceed to steal energy from all the worlds. Since our heroes don't know where Calamitous' lair is, they start with saving all of their worlds first.
They go to Amity Park first and find Vlad. Vlad reveals that he uses his ghost-portal to steal ghost energy from the Ghost Zone. Vlad has also captured Danny's parents. Then, he sends the heroes to the Ghost Zone Prison. The Nicktoons survive in the prison and defeat Walker. They break out of the prison through a portal and end up in Fenton Works. They see many Amity Park civilians possessed by ghosts, but manage to push them out. The Nicktoons go to the Amity Park Graveyard, which is a shortcut to Plasmius' castle. When they go in, Jimmy realizes that there are generators that help Vlad keep the portal open. They find the generators, and destroy them, shutting off the portal. When they find Vlad, the Nicktoons defeat him and save Jack and Maddie Fenton without them noticing the Nicktoons. They also find out that the Syndicate is building something.
Next, our heroes go to Bikini Bottom to fight Plankton. They meet Sandy and follow her to the Krusty Krab. Sandy tells the Nicktoons that they should find some guards which should help them find Plankton and the Jellyfish Factory. Fortunately, they found the guards. Sandy then explains that Plankton uses the harvesters to capture jellyfish, and is extracting power from their sting in the factory. Plankton also captured Mr. Krabs. Sandy told the Nicktoons that they must go into the Jellyfish Factory and free all the Jellyfish. After Timmy asked if they have any secret agents (since he thought that it's like a spy movie), Sandy said that they have an agent in Jellyfish Fields, who is revealed to be Patrick, but he's been captured by a Jellyfish harvester. After destroying all the harvesters, the Nicktoons go to the factory, but during the journey, they find themselves on the Flying Dutchman's ship and the Flying Dutchman is going to make them his new crew for all eternity. Luckily, the Dutchman frees them after they bring back his old crew. When the Nicktoons arrive at the Chum Bucket, they free Patrick and all the Jellyfish by opening the emergency vents. Later, they went up to the top of the Chum Bucket, they beat Plankton and rescue Mr. Krabs. The Nicktoons find out that the villains are extracting energy for a Doomsday Device.
In Dimmsdale, the Nicktoons see Crocker has made the fortress made of gold. They also find a rainbow of pure Fairy Magic from the Fairy World that is ending there, so they go in. After they re-activate the prisms, they get transported to Fairy World, where they meet Jorgen Von Strangle. Jorgen explains that Crocker is extracting the magic from the Big Wand to feed the Doomsday Machine. After freeing the fairies, they go to The Big Wand, where they defeat Crocker. Danny figured out that every time they beat their enemies, they're running away, which was a part of a plan.
Finally, the Nicktoons return to Retroville, where Jimmy finds Cindy in his lab and he also receives a message from Calamitous that they've almost finished the Doomsday Machine and the Nicktoons can't stop them. After SpongeBob notices that Goddard has fleas, Jimmy says that Goddard doesn't get the fleas. Then, he figured out how Calamitous could spy on him; he was using a flea-bot inside Goddard. So the Nicktoons shrink themselves down and go to Goddard's stomach. They beat a lot of mini flea-bots throughout Goddard, and Danny, Timmy, and SpongeBob gain Goddard's trust. They go to Goddard's head and beat the giant flea-bot. Jimmy used the flea-bot's circuitry and locate Calamitous' secret lair, which is situated under an old warehouse. When they get to Calamitous' Doomsday lab, they find The Syndicate in a wheel-like machine that shields them. They beat the Syndicate but they see that the Doomsday Device is still counting down to destroy the universe and it can't be stopped. Luckily, SpongeBob unplugs the Doomsday Machine and saves the universe.
After putting Calamitous and Plankton in jail, the Nicktoons said themselves goodbye, but before they went, Jimmy gave them the Neutronic Recallers in case of another event like this. SpongeBob said that Jimmy can visit him any time he likes, but then he said he should get going, so he won't be charged by Mr. Krabs for wasting his time, Danny gave Jimmy a copy of the Fenton Thermos, then Timmy thanked Jimmy for lending him his Hyper-Cube for holding Crocker until Timmy and his fairies get back to Dimmsdale. After this, Jimmy says a familiar line: "Cindy, get out of my lab!"
The game starts with Jimmy Neutron appears at the beginning. It is said that he has invented the Neutronic Reality Projector, which allows him to open doors to other dimensions. However, Professor Calamitous has copied the plans. He has gathered three villains: Vlad, Plankton, and Mr. Crocker. Together, they have created a Doomsday Device, which is a device capable of destroying the multi-verse. It requires fuel from each of the universes to run. Jimmy somehow figures this out and makes his own super-team of Danny, Timmy, and SpongeBob. Jimmy explains to the heroes that the Syndicate of Evil is stealing ghost energy, jellyfish energy, and magical fairy hologram energy. He tells the group that they need to work together to stop the Syndicate.
The game opens up with Jimmy as the playable character. He is in his lab, facing a portal, which has been created by the Neutronic Reality Projector. The player can choose which character the player wants to us. If Jimmy is not selected, he will appear in the lower right-hand corner of the opposite screen. Once the player enters the portal, the option is Fenton Works.
Here, Danny explains that Vlad has taken control of Fenton Works' ghost portal. The player starts in a field near Fenton Works. Jimmy can use his Jetpack to fly up in the air. The player goes through the town until the player reaches Fenton Works. They enter the home. Here, the house is invested by ghosts, which the player needs to get rid of. The player eventually reaches Danny's room, where there is a ghost portal open, which is causing ghosts to appear in the room. Jimmy can shrink enemies using his Shrink Ray. The portal can be destroyed by the player. After the room is done, the next destination is the lab. Here, the player fights ghosts until the player reaches a door to another part of the lab. Danny says that someone has tampered with the circuity and locked the door. Jimmy tells Danny that he can fix it. The player, as Jimmy, then fixes the door. Once inside, the player fights more ghosts until the player reaches the ghost portal.
After Danny sends the ghost back to the Ghost Zone, the heroes head back to Jimmy's lab. Here, the player can either play the mini-games they have unlocked or enter the portal. Once the player has entered the portal, the player can now go to Casper High. The player then has to get through a long road, filled with ghosts, until the player reaches Casper High. Inside, there is more ghost to defeat. The player goes down a long hallway and then into a classroom. After getting through the room, there is another hallway the player has to get past. The next room is the cafeteria. After getting through the cafeteria, the player has to get through the football field. Here, there is another portal.
Like the last time, once Danny puts the ghost back into the portal, the heroes go back to the lab. The next destination is Vlad's Castle, which in this version is his mansion. Vlad has managed to move his mansion to Amity Park. He asks who is there to stop him and Danny says, "Danny Phantom..." and all of the heroes say, "And friends!" The player then has to get through Vlad's yard, which is infested by ghosts. Inside, the player goes a few feet and Danny says that Vlad is trying to attack his dad. The heroes stop Vlad's shots. Timmy says that Vlad is getting away. Jimmy tells the group to go after him. The player then goes through the mansion to stop both ghosts and Vlad from escaping. Eventually, the player reaches Vlad's lab. Once the player gets through the lab, the player has to stop Vlad. Once he is defeated, he leaves. Jimmy says that they should get back to his lab.
The next destination is the Kelp Forest. Jimmy offers his Neutronic Air Gum and Danny and Timmy take it. The player travels through the Kelp Forest, fighting off Jellyfish. Eventually, the enemies are Tough Guys. Eventually, the heroes find out that the Kelp Forest is not the location of the Jellyfish Sting Extractor. The heroes then head back to the lab.
The next destination is Bikini Bottom, more specifically, Conch Street. They fight bullies and end up somehow being transported to Jellyfish Fields to stop Plankton from hurting Patrick. The mini-game is similar to the one with Vlad and Mr. Fenton. After saving Patrick, the group is transported back to Conch Street. Here, Patrick tells them that the bullies were going to the Krusty Krab. After going through a tunnel in Patrick's house they make it to the Krusty Krab. Here, there are bullies everywhere. There are also large Rufuses. After defeating the enemies, the player has to collect a key. After the player does this, the heroes discuss going back to Conch Street because Squidward might have gone home and been in trouble. They also believe the bullies might have a clue as to where the Jellyfish Sting Extractor is. They get back to Conch Street and enter Squidward's house. Here, only SpongeBob's house key can found. Jimmy recaps the fact that they don't know where the Jellyfish Sting Extractor, Squidward, or Plankton is. SpongeBob suggests they watch the news to see if anything's on. However, it is broken, so Jimmy suggests they go to SpongeBob's house. The heroes do so. Here, they find enemies. After defeating them, the heroes check the news, which is talking about the Chum Bucket. The heroes realize that is where they need to go. They head back to Jimmy's lab.
The next destination is the Chum Bucket. After going through a maze, fighting bullies, the player reaches the Chum Bucket. Inside, there are more enemies. After working there way through the Chum Bucket, they destroy the Jellyfish Sting Extractor and soon find Plankton. Here, the player has to defeat Plankton, who is in a Robotic Jellyfish. After defeating Plankton, the heroes return to the lab.
The next destination is Dimmsdale. Here, Timmy says that he doesn't know where Crocker is, so they have to travel the whole town. Eventually, the reach the Dimmsdale Dump. After going through the dump, Timmy remembers the school might be an option. They head back to the lab.
The next destination is Dimmsdale Elementary School. Here, Jimmy gets some transmissions that say that Federal Agents are around the school. After getting past them, the heroes enter the school. Here, more federal agents are present. After getting through the halls, the heroes reach Timmy's room, where Mr. Crocker is going to harm Chester with lasers from his Heat-Seeking Fairy Googles. After stopping Crocker, agents appear in the room. After getting through the room, they find themselves in the Original Crocker Cave, which has been redesigned as a transporter to Fairy World. The heroes head back to Jimmy's lab.
The next destination is Fairy World. Here, Crocker has released Anti-Fairies. The player gets through the first part of Fairy World and enters a building, where more Anti-Fairies are. After going through the one-roomed building, the player enters the second part of Fairy World. In this part, the heroes have to save the Fairies by putting them in bubbles. After going through the section of Fairy World, the player finds Crocker. The heroes need to stop him from releasing evidence of Fairies and taking over Fairy World. After defeating Crocker, the heroes head back to the lab.
The next destination is Jimmy's House. The player starts in Jimmy's room. The goal is to find Goddard, who has been kidnapped. The enemies are walking pants and lasers. After leaving Jimmy's house, the heroes have to fight through the yard, collecting computer chips to power up the tracking device. Once it is powered up and Goddard's location is found, the heroes head back to the lab.
The next destination is the Retroville Mall. The heroes have to fight their way to the mall. Once inside, they have to fight their way to the next room. They are transported to the Candy Bar. Here, there are more enemies. Eventually, the heroes find Goddard. Calamitous is about to shoot Goddard with a laser on a platform, which he is on. The heroes stop him and head back to the lab.
The final destination is Retroland, a theme park. This is where Calamitous and the Doomsday Machine is. The heroes go through the parking lot and then into the admission area. The enemies are robots. They enter the park. After going through that part of the level, the heroes find themselves at a Ferris wheel. After going through that part, they two more rides and a maze to get to them. The important ride is the Bat Outta Heck ride. Here, the player has to go through the ride to find Calamitous, who is in a ship. Eventually, a countdown starts and the player has a minute to defeat Calamitous. After defeating Calamitous, he flies away. The heroes disarm the Doomsday Device and Jimmy gives them all Neutron Recallers.
Game Boy Advance
The set-up to this version is the same as the DS version. There are two differences: 1. In the DS version, it is stated that the Doomsday Device can destroy the multi-verse. In this version, it does not. 2. In the DS Version, Jimmy calls it "magical fairy hologram energy." In this version, he just calls it "fairy energy."
The first location is Amity Park, more specifically, Casper High. Here, Vlad has unleashed a ghost army. In this version, the player has two characters at a time, which they can switch back and forth. There is three ghost portals that the player has to destroy in this level. The player goes around the campus and destroys ghosts. Jimmy's main attack is a freeze ray. The player also goes around collecting nanochips to open the portal at the end of the level. Much like in the DS version, Jimmy can also use his jetpack. The characters can also be switched at Teleporters.
The next location is the Fenton Works. Here, Danny says that they need to shut down the ghost portal because that is how Vlad is draining ghost energy. The player then goes through the lab at Fenton Works and defeats ghosts.
The next location is Vlad's Chateau. Like the DS version, Vlad has brought his mansion to Amity Park. Unlike in the DS version, the level is just a boss fight with Vlad. After he is defeated, he goes away.
The team then goes off to the next world, which is SpongeBob's world. The first location in this world is Bikini Bottom. Here, Jimmy gives Danny and Timmy the Neutronic Air Gum. Plankton appears saying that he cannot let them destroy his Jellyfish Sting Extractor. He then tells them that his thug fish will take care of the heroes. The heroes go around part of the ocean, defeating enemies. They find portals, but this time, they release Jellyfish, instead of ghosts. Eventually, the heroes reach Conch Street. They enter SpongeBob's house, which has enemies and portals to other parts of his house. Once the player completes the level, Danny says that the thugs are taken care of and SpongeBob tells them that Plankton is at the Chum Bucket.
The next location is the Chum Bucket. Here, Danny says that the Chum Bucket has guards all around it. He asks how they are going to shut down the portal. Jimmy says that with his Neutronic Sizeifer, they can shrink themselves and get inside. The heroes then go through the Chum Bucket and defeat Jellyfish and Plankton family members.
After going through the Chum Bucket, the heroes face Plankton. However, he has used Jimmy's Neutronic Sizeifer to make himself larger. The heroes defeat Plankton, set the Jellyfish free and it is off to the next world, which is Timmy's world.
The first location of Timmy's world is the Turner House. Robots have invaded the house. Jimmy says that they are Calamitous' Clambots. Timmy thinks they are there for a portal to Fairy World. Danny says that he does not believe in fairies. The heroes then go through the house, fighting Clambots and Nega Timmys. At some point, the heroes find a portal that lets Clambots out. Much like SpongeBob's house, there are portals in Timmy's house. After going through the house, they go through a portal to the next location, which is the Dimmsdale Dump.
Here, Jimmy says that the robots are coming from Dimmsdale Elementary School. Timmy says there is a shortcut through the Dimmsdale Dump. Here, the enemies are laser guns. After they go through the Dump, they enter a portal to the next location, which is Dimmsdale Elementary School. Here, Timmy wishes that he knew who was responsible for the robots and Wanda grants his wish. They find out that it is Mr. Crocker. They fight Crocker and Nega Timmy. Afterward, Crocker runs away. Jimmy says that at least Crocker won't be using any fairy energy for the Doomsday Device.
The heroes return to Jimmy's lab. Here, Calamitous reveals that he has turned Jimmy's inventions against him, notably the Nano-controlled Pants. The heroes fight through the lab, fighting Clambots, Nano-controlled Pants, and laser guns. Like Timmy's world, the portals contain Clambots. Like SpongeBob and Timmy's houses, there are transporting portals in the lab. After reaching the end and going through a portal, the heroes end up in Subterranean Caves. Here, the same enemies as the last area are here. After going through the Caves, they end up in a portal to Calamitous' Secret Lair, where they find the Doomsday Device and the Syndicate of Evil. Here, their heroes fight Calamitous, who is in a ship similar to the one in the DS version, Vlad, large Plankton, who is accompanied by thug fish, and Mr. Crocker, who is accompanied by Nega Timmy, individually. After being defeated, Calamitous says that they have been defeated, but the Doomsday Device has not been turned off. Jimmy finds the off button as presses it. Like the other two versions, Timmy, Danny, and SpongeBob receive Neutronic Recallers at the end of the game.
In the console versions, a player can play by him/herself with three CPU's, or have up to three friends who can play along. In single player, the person playing can switch between the four characters at any time in the game by using the Directional Pad (that little pad thing that looks like a plus (+) sign that's either over the left analog stick for the PS2 controller, or under the gray Control Stick on the GameCube controller). Every character's health and Special Ability Power (SAP) is represented by the two combined arrow-point shaped bars near the character's face icon on the bottom left corner of the screen. In single player, depending on where the arrow is pointing, that's the direction to push on the D-pad to switch to the corresponding character. The green bar represents health, the purple means SAP. A character's health lowers when they take damage from things such as enemies. When a character's health lowers to an especially low degree, the character says they need help, and the character's face icon changes to a more worried and tired icon that flashes red. If a character's health depletes completely, then that character dies, not affecting the rest of them, but costing that character a life. If a single character loses all their lives, the player gets a game over, because all the levels in the game have sections that require the now dead character's special powers. More health can be earned by picking up the green orbs of it that enemies drop when the player(s) defeat(s) them. There are certain tasks that only a certain character can do, and performing these special abilities will deplete the character's SAP meter. For example, SpongeBob is needed to use Bubble Bombs to blow up seemingly breakable walls and pillars, Danny is needed to use Ghostly Wail to shatter glass, Timmy is needed to use Freeze Glove to freeze water instantaneously, and Jimmy has to shoot down objects with Neutron Flare. If a character completely depletes their SAP, they can no longer perform that ability (or the rest of their special abilities) until more SAP gradually comes back over time, or the player collects the purple orbs of it enemies drop when they're defeated, exactly like how recovering life works. There are two kinds of fighters to play as. SpongeBob and Danny both use their hands to attack, while Timmy and Jimmy send out projectiles. SpongeBob and Danny are better for defeating enemies faster because they both use close-quarters combat, but are more likely to get hit if there's a large crowd of enemies. And while Jimmy and Timmy use projectiles so they can damage enemies from a farther distance allowing them to stay out of range from enemy attacks, it will most likely take longer to kill them due to the projectiles lack of strength and speed.
Goddard can be found in all four worlds so he can upgrade the player's weapons and abilities.
The PlayStation 2 and GameCube versions have the same gameplay, while the Game Boy Advance and Nintendo DS versions each have their own gameplay style.
This is the only game in the Nicktoons Unite series whose Nintendo DS version is not developed by Natsume.
Carlos Alazraqui, who voices Denzel, previously worked with Tom Kenny, on Rocko's Modern life, where the former voiced Rocko Wallaby, while the latter voiced Heffer Wolfe.
In the Game Boy Advance version, in Timmy's Home level, when Timmy says, "Hey, why are there robots in my house?" the player can see Jimmy's room in the background.
In the Game Boy Advance version, Denzel Crocker is misspelled as "Denzil Crocker" in the intro.
In the console version, Wanda says that she and Cosmo have lost their powers. However, throughout the game, she and Cosmo use magic as Timmy's main attack. In addition, she and Cosmo use magic to poof into the scene right before she says that she and Cosmo have lost their powers.
When Danny goes into his invisible form, he states, "Going Ghost!" However, this is improper because this is what he says when he goes from human to ghost form.
At the beginning of the scene that introduces the prism in the level, "Crocker's Fortress," it is written that Timmy calls Fairy World, "Fairy Land."
In the console version, in the second cutscene, each of the members of the Syndicate is shown on Jimmy's computer. Professor Calamitous is shown in 2D, as opposed to CGI, which is the animation that his show is in.
In the console version, in the Krusty Krab cutscene, SpongeBob says, "Wow. A secret agent, I wonder who it could be.", but the caption writes, ""Wow. A secret agent, I wonder who it could be?".
In the Nintendo DS version, SpongeBob's door is wooden and his path is just a dirt path. The flowers around his house are also missing.
In the Nintendo DS version, Patrick's wind vane is not bamboo, but metal.
In the Nintendo DS version, the interior of the Krusty Krab looks almost completely incorrect.
In the Nintendo DS version, in the level select menu, the Chum Bucket is made into one word, not two.