Messed-Up Worlds is the story mode of Nickelodeon Ultra Struggle.
The player is able to peek into a vial through a microscopic view. They can see two green, glowing cells. One is twitching, getting a shade darker every three seconds. It suddenly grabs the other cell and eats it, growing twice the normal size.
SpongeBob SquarePants wakes up to his boat horn alarm. He explains to Gary, his pet snail, how today is the 175th anniversary of the founding of Bikini Bottom. There will be a party at the Krusty Krab, so he decides to invite all of his friends.
At the party, everyone is having fun until Plankton barges in, wanting to steal the secret formula as per usual. SpongeBob and Patrick Star fight him, and he flees. However, a large alien fleet soars towards the Krusty Krab. SpongeBob and Patrick try to investigate, but SpongeBob gets sucked into a portal. Patrick yells his name as he falls through the portal, becoming more 3D-ish every second...
New York City
The Ninja Turtles -- Leonardo, Raphael, Donatello, and Michaelangelo -- are eating pizza and playing video games when an alien warship approaches their lair. Master Splinter tells them to stop the aliens, so they grab their weapons and head up to the warship.
The ship belongs to an extraterrestrial species known as the Irkens, as Donnie realizes. The turtles fight Irken cadets until they reach the Almighty Tallest, who do not fight them directly. (So lazy, am I right?) Instead, they bring out a large Kraang alien to fight the Turtles for them. After defeating it, the Tallest flee via Voot Cruiser. Leo finds SpongeBob lying down on the floor -- and he is gasping for water! The turtles quickly carry him back to the lair, as a mysterious robot watches them leave.
In the lair, the Turtles give SpongeBob some moisture spray, which Donnie has made specifically for a situation like this. SpongeBob begins to wonder where he is, and Leo explains that he has entered an alternate dimension. They team up to find a way back to Bikini Bottom.
Cutscene 1: Foot Lair
The Shredder steps into a meeting room, and sits down with his new allies -- Plankton, Vicky, Professor Calamitous, Puma Loco, Vlad Plasmius, Vexus, Snaptrap, Fire Lord Ozai, and the Almighty Tallest. He begins to explain that his scientists have created a lifeform that can grow with everything it eats. It has been dubbed Mutation Z, and the villains will use it to wreak havoc all around the Nickeloverse.
Timmy Turner and Chloe Carmichael are walking to school, talking about their plans for summer vacation. Timmy wants to hang out with his best friends Chester and A.J., as well as his love interest Trixie Tang. Chloe thinks Trixie's name sounds nice, and would love to meet her.
All of a sudden, they find Bebop and Rocksteady terrorizing the school. Chloe asks Timmy if he knows how to fight. "Kind of," Timmy replies. "I've got some traces of dark magic left over." Chloe backs up, nervous about how the fight will turn out. Then, Timmy calls up Cosmo and Wanda to assist him, and they fight Bebop and Rocksteady, eventually beating them.
Timmy and Chloe begin to wonder how the mutants got to Dimmsdale, and agree to wish for a trip all around the multiverse.
The Turtles' Lair
SpongeBob is cooking when he hears noises from around the lair. Thinking it's a robot, he tries to warn the Turtles, but they don't believe him.
The robot from earlier approaches him with a robe. They fight, but SpongeBob eventually falls for his own fear. He runs away from the robot, and drops his spatula in the process. The robot chases him into a corner... and gives him the spatula. Confused, SpongeBob asks the robot for its name.
The robot removes its robe and reveals itself as XJ-9, otherwise known as Jenny Wakeman. She explains that she's caught wind of a devastating scheme, and was sent by her mother to find as many interdimensional heroes as possible. Jenny states that SpongeBob was the first on her list.
The Ninja Turtles rush in, saying that they heard SpongeBob screaming for help. Raph attacks Jenny, thinking she's working with the Almighty Tallest, but Leo pulls him away. Timmy and Chloe then show up, and the eight heroes agree to find out what's going on with the dimensions and stop whoever is behind it.
The heroes split up, with SpongeBob and Jenny heading to Tremorton. They stop by the Wakeman residence and pick up an exosuit to make SpongeBob look like a human.
They then visit Mezmer's Nightclub, and Jenny tells SpongeBob to try and fit in with the crowd. The latter, going by the name "Bob", walks up to the bar. He meets Brad Carbunkle, who hands him a soda. As "Bob" guzzles up the soda, a popular dance tune in Tremorton comes on. At the stage, the electronic music artist, DJ Serpent, prepares his latest song -- "Like A Jellyfish".
SpongeBob, still in the "Bob" disguise, thinks the song is very familiar. But before he can start dancing, an army of Toybots barges into the club. SpongeBob recognizes them from one of his past interdimensional adventures, and is willing to go up against them. He grabs a nearby hair dryer and dries off his exosuit, much to the crowd's dismay.
A battle similar to the online game Dance Off, Battle On begins, where SpongeBob and Jenny must defeat enemies to fill up the dance meter and unleash a "dance attack" that distracts the Toybots.
After the battle, Brad drives them over to his house. The whole time, he rants about the fact that Jenny brought a talking sponge into Tremorton. After SpongeBob tells him that there are mutant turtles as well, he goes on talking about other strange things that have happened to him -- but none of them are stranger than this.
Brad picks up Tuck, and Jenny asks where their parents always are, because she has never gotten a chance to see them. Brad tries to come up with an excuse, but he stutters and eventually appears to be sad. They head for their next destination, as Brad & Tuck begin to wonder what happened to their parents...
Lincoln Loud rushes out of his room, sliding down the staircase railing and into the living room. He explains (to the player) that it's almost time for him to watch the first episode of "Ace Savvy" -- the comic book is so popular it's getting a new TV series. But his sister Lynn is already watching the "Hyper Dish", a football championship. Luna is jamming with her electric guitar, and Lisa is doing weird experiments.
Lincoln approaches Lynn, politely asking her if he can have a turn watching TV. When she declines, he questions why she has been watching so much of the Hyper Dish and not letting her siblings have turns. Lynn states that when the Hyper Dish is on, she doesn't care what else is on. Luna butts in with her wish to watch the ultimate "Fear! at the Nightclub" concert, and Lisa wants to see the wildlife documentary, "The Very Craziest". It then turns into a fight for the TV remote, and Lisa drops one of her potions on it. When Lincoln accidentally presses the power button, the screen transforms into a portal, sucking them in.
Lincoln, Luna, Lynn, and Lisa find themselves in a world of popular television channels. Just as they are about to go their separate ways, Baxter Stockman soars over to attack them, prompting a battle.
Afterwards, Stockman flies back through a portal. Lisa determines that some of these channels exist in other worlds as well, forming gateways between dimensions. Lincoln decides that they have to find a way out of the TV Realm.
The Flying Dutchman arrives via portal, and sends out an army of ghosts to terrorize the civilians. Danny Phantom and Sam charge into battle, ready to "bust his ecto", as Danny puts it.
After the fight, Timmy and Chloe enter Amity Park. They team up with Danny and Sam to rescue any civilians in danger. Then, the rockstar ghost known as Ember McLane drops in and reveals that she has powered her guitar with fairy dust. Thus, she doesn't need to hear her name to gain more energy. Timmy, Chloe, Danny, and Sam chase her into the Flying Dutchman's ship, where they fight a squadron of mutated Syndicate Grunts. Danny tries to trap Ember in an ectoplasmic thermos, but she escapes and flies away.
The heroes find an old TV with a remote. Cosmo & Wanda return, pointing out that it still works. Timmy gets an idea -- he wishes that he could go inside the TV and look for more heroes. The fairies grant his wish.
Cutscene 2: TV Realm
Timmy, Chloe, Cosmo, Wanda, Danny, and Sam meet up with Lincoln, Luna, Lynn, and Lisa in the TV Realm. Danny is serious and tries to explain their situation, but Timmy and Lincoln seem to automatically form a bond thanks to their common interests. They jump into several channels and talk about comic books, video games, etc. Danny sighs; he knows that they have stopped taking this mission seriously.
Arnold Shortman and Gerald Johannsen are hanging out at Antonio's Pizzeria. Arnold tells Gerald about the map he found a few days ago -- it shows San Lorenzo, where his parents might still be living. Gerald is fascinated, and says that maybe he'll have a better chance of understanding who he is. Arnold agrees, stating that he already knows a lot from those stories his grandfather told him.
After they eat, they head outside to see a strange dog-like monster wreaking havoc throughout the town. The monster -- Rahzar -- attacks Arnold and Gerald, but Donnie charges over and knocks him away with his staff. The Ninja Turtles team up with Arnold and Gerald to fend off Rahzar.
They see an alien warship approaching. A glowing hologram of Vexus shows up in the middle of the city square. She explains that the Cluster species has split up due to civil war. One side is led by her, and the other is led by her "traitorous" daughter Vega. Vexus is prepared to obliterate Hillwood if its citizens don't comply to her demands. When she realizes that they won't, she sends a squadron of Cluster Drones to wipe them out. Fortunately, Misty stops them; she tells Arnold, Gerald, and the Turtles to hurry up and "get out of the open".
Jimmy Neutron and Cindy Vortex exit the arcade with the numerous prizes they've won. Cindy asks Jimmy if he's had any luck looking for Sheen Estevez, who vanished with Jimmy's rocket a while back. He replies that he's getting close, but there is still something missing... and he doesn't know what it is.
They come across Professor Calamitous, who exclaims that they are very lucky to be here. Jimmy asks him what he's up to this time, to which he states that he's getting ready to take off in his spacecraft and invade the planet Zennu. Jimmy says he's not going to let that happen -- with that, he and Cindy fight Calamitous and break the spaceship. Calamitous is angry, and flees, yelling at Jimmy for losing his only way to find an old friend.
Jimmy ponders this statement, and realizes that Sheen must be on Zennu. Suddenly, he sees the other heroes (the teams of SpongeBob, Arnold, and Timmy) arrive through separate portals. Lincoln is amazed by the depth he has received in this dimension, as are his siblings, Arnold, and Gerald. Jimmy greets Timmy, and says that he hasn't spoken to him in a long time. He tries to give him a fistbump, but Timmy declines the offer, stating he has a new interdimensional best friend -- Lincoln. Jimmy argues that he can't just break their bond because of someone he barely even knows, but Timmy and Lincoln ignore him, heading out to the playground without him.
A fleet of Irken ships heads for Miracle City. El Tigre, seeing the trouble they are causing, springs into action with his friend Frida. They face off against some Irken soldiers, and soon meet the fleet's commander...
Zim explains that his new boss, Shredder, offered him a "big" position in the new multiverse regime if he helped him. He also states that the Irkens have recently formed an alliance with the Kraang and Vexus's loyalist Cluster faction, primarily to provide ground-breaking technology for their forces.
After a battle between El Tigre and Zim, the latter proclaims that this war is not over yet, because Shredder is working on something really big...
SpongeBob, Jenny, Leo, and Jimmy walk down the street, discussing their next move. Jimmy has explained his situation to the other three, and they are willing to help him, especially SpongeBob. After all, he has had some interdimensional experience with Jimmy.
They begin to look for some parts to build a rocket, so they can reach Zennu and find Sheen. Meanwhile, Timmy and Lincoln are merely relaxing at the park, talking about who would win in a battle, Crimson Chin or Ace Savvy. Timmy says he'll be right back, and hides behind a bush. He summons Cosmo and Wanda, and wishes that Crimson Chin and Ace Savvy were real. Wanda says they don't know who Ace Savvy is, so Timmy shows them one of Lincoln's comic books. The fairies grant his wish, and each comic's pages begin to flap wildly.
In Jimmy's lab, Jenny finds the old portal machine used in Nicktoons UNITE!. Jimmy reccomends she doesn't mess with it; it hasn't been activated for a long time, so if anyone were to suddenly bring it to full force, it would emit neo-radioactive gas -- or, as he dubs it, NRG. This gas is found all over the Nickeloverse, and a few other multiverses as well. Jimmy explains that NRG is usually absorbed into living matter, but if there is too much in a certain area, it will form a circular piece of metal almost like a token. When a living being picks up one of these tokens, it dissolves back into raw NRG and is absorbed, giving the entity a sort of special essence that he can't explain.
As he is about to go into further detail, Crimson Chin and Ace Savvy break through the roof of the lab. They fight, shattering equipment and even knocking over Jimmy's girl-eating plant. Timmy comes in and sees the plant, taunting Jimmy because he thinks he was going to use it on Cindy. Jimmy says that he was, but he doesn't want to anymore. Lincoln barges in with Luna, Lynn, and Lisa, screaming "PUSH ALL THE BUTTONS!" Everyone except SpongeBob, Jenny, Jimmy, and Leo causes problems in the lab, until finally Lynn activates the portal, sarcastically saying, "Oops! My bad!"
NRG fills the lab, turning everything into shiny orange metal. The heroes escape before it can cover the entire area. They suddenly run into a group of Kraang aliens, and SpongeBob, Jenny, Leo, and Jimmy fight them while the others flee -- except Crimson Chin and Ace Savvy, who continue fighting each other.
Donnie opens a portal, and the heroes get inside, with Tiger Claw watching them leave.
Cutscene 3: Shredder's Chamber
Tiger Claw meets up with Shredder, telling him about the children who have been brought together by the danger spreading throughout the dimensions. Shredder tells him to let them be that way; there is no one to help them. Tiger Claw then mentions that the Ninja Turtles are, and Shredder turns furious, slashing at any structures around him to let out his anger.
He asks for any other details, and his student says they were all accompanied by a robot. Shredder grabs him by the neck and yells, "WHAT ROBOT?!"
Spirit World/Republic City
Korra explores the Spirit World with her good friend and love interest Asami. They are having fun until a strange portal opens up, releasing several ghosts from the Ghost Zone. Korra forces them back with bursts of water, but it's too much for her. Suddenly, a youthful Aang shows up, using airbending skills to split them up. He tells Korra that thanks to some strange things going on in their world, he has somehow been revived. They gain back their physical bodies so they can head down to Republic City.
In the city, Aang and Korra fight more ghosts, and the latter says that "these guys aren't the spirits I'm used to". They soon meet the spirit form of Ozai, who has gained his bending back due to one of Shredder's meditations. The two Avatars face off against him, and they escape as Republic City falls prey to the ghosts.
Zim arrives in the Fairy World plaza and looks for fairies to mutate. After collecting 25 fairies, he comes across Jorgen von Strangle, who chooses not to fight him. Instead, he shoves him off the clouds. Zim must find a way to propel himself back up; afterwards, he sprays mutagen ooze all over Jorgen, who is stung by a bee a few seconds later.
Police cars swarm the streets as a group of criminals cause trouble. T.U.F.F. agents Dudley Puppy and Kitty Catswell fight them off, eventually locking some of them up. They soon see a fleet of Kraang ships bombing the city and head out to stop it, with Timmy, Lincoln, Jimmy, and Mikey joining them.
An arena-type battle begins, with three waves of Petropolis criminals and Kraangdroids. After the third wave, Kraang Subprime demands to know the whereabouts of XJ-9. Jimmy says he won't tell him anything, and Dudley adds that he doesn't know who or what XJ-9 is. Subprime states that it doesn't matter anyway -- he can scan any territories captured by the Syndicate of Devastation using special technology the Irkens set up. He soon discovers that XJ-9 is in a recently captured city under the sea...
Bikini Bottom II
SpongeBob, Jenny, and Leo (who is equipped with a scuba suit) arrive in Bikini Bottom, which has been completely overrun by the Kraang. Leo suggests they search for survivors, and they go out to do so. SpongeBob finds Patrick hiding in his rock-house, and he joins the three (after being convinced to overcome his fears).
They split up to find the Kraang fortress, with Leo and Jenny heading downtown and SpongeBob and Patrick checking on their friends' houses. The downtown group finds nothing, but Patrick points out that Sandy Cheeks's house looks... different. SpongeBob and Patrick put on their water helmets, and Leo takes off his scuba suit. The four walk into Sandy's yard; Leo wonders how Jenny survived under the ocean without short circuiting, and the latter says she had a bubble shield equipped in her system.
As they look around, they realize that Sandy's tree is very dark. Patrick begins to cower, and is about to scream until SpongeBob calms him down with a paper bag to breathe in. However, Patrick was right to be scared, because a mutated Sandy growls at them. They escape through the front door, but Sandy breaks out, revealing that she has become a fish-squirrel hybrid thanks to the ooze. She chases all four of the heroes, with Jenny firing occasional blasts to stun her. Leo finds a vial of retro-mutagen and an injection needle lying in front of a garbage can, and uses them to bring Sandy back to her normal form. However, she is not wearing her underwater suit, so they rush her back to her house (within a five-minute time limit).
After Sandy recovers, Leo asks her if she knows anything about the Kraang since they took over. She replies that she spied on a few Kraangdroids talking about a fortress in a jungle. Jenny states that according to her dimensional database, there is one hidden temple in a world that has been isolated for decades, and they go out to find it.
Tak helps his fellow villagers herd a group of goats, then goes around the village asking if they've seen any danger in the area. Two elders warn him of the rise of a new threat... and the return of an old enemy. They tell him to head into the depths of the jungle and collect five crystal fragments.
He then takes them back to the elders, who bestow magical powers on them, thus bringing them together like magnets. They explain that this new weapon has strange abilities that are very similar to those of the Staff of Dreams; it can open portals between realms, including the worlds of dreams and nightmares. The elders tell Tak to stop the rising terrors that may soon threaten the entire universe.
Raph and Luna enter Dimension HB-15BW, locally known as the Bigbark Woods universe. They meet up with Harvey Beaks, who tells them that the town's bank has been robbed.
They search through the city, questioning citizens and asking them what happened and what exactly they saw. At long last, they find the culprit -- Casey Jones -- and chase him through the forest, eventually catching up to him and beating him.
Raph asks Casey why he robbed the bank, and the latter replies, "I had to pay for the fruit somehow." Harvey points out that he was eating furberries, to which Casey responds with disgust, grabbing a jug of water to rinse the fur out of his mouth. He decides to join Raph, Luna, and Harvey if they can keep him away from the Bigbark Police.
New York City II
Donnie and Lisa are on the lookout for Foot soldiers. They see a suspicious-looking truck swerving through the streets, and head down to investigate.
Lisa finds a trail of ooze, and believes the truck may have left it behind. She and Donnie follow the trail to the courthouse and try to sneak in. Donnie detects heat signatures in the courtroom, and peeks through a vent to find a group of Foot ninjas... and they're holding Lucy Loud hostage!
Donnie and Lisa break in and fight the ninjas, but they accidentally spill ooze all over Lucy. A crow perches on her shoulder, and she becomes a horrifying crow-like mutant. She exclaims that she is now stronger than she could ever be as a human, and names herself Freakshow. Then, she soars off into the night as Donnie and Lisa watch, shocked.
Cutscene 4: The Lair
Lincoln returns with Timmy and Jimmy, and tells Donnie that Mikey had to stick around with T.U.F.F. and fight Kraang Subprime. Donnie gets a distress signal directly from Shredder's lair, and determines it's coming from a cell phone. After he decodes the signal, he realizes it was sent by Lori, the oldest Loud sibling.
Even Lynn, who was sleeping on Raph's bed, jerks awake when she sees Lori crying for help from her phone camera, as most of the other Louds huddle around her. Shredder snatches the phone out of her hands and places it in front of him, forcing Lincoln, Lynn, Jimmy, Timmy, and Donnie to watch as four of the sisters are mutated one by one.
- Lana transforms into an ugly toad, dubbed Croakon;
- Luan becomes a horribly deformed clown, and is named Jester;
- Leni is mutated into a giant tarantula called Cobweb;
- and finally, Lori turns into a menacing bald eagle, going under the codename Shrieko.
Lincoln screams with terror, and Shredder announces that he has a new ally in training -- Lola. With these words, Lola releases the new mutants, who enter different dimensional portals as Shredder smashes Lori's phone.
Lincoln hides in Donnie's room and cries, and Lynn tries to cheer him up. Donnie promises that he will get their sisters back, no matter what it takes. In the meantime, Leo is at a hidden temple with SpongeBob and Jenny, and he needs to keep track of them. Master Splinter tells Lincoln, Lynn, Jimmy, and Timmy to find Lucy first, because she may be somewhere in this dimension.