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The second story of the game.
San Francisco Bay
The Bare Bears -- Grizzly, Panda, and Ice Bear -- are trying to become famous again, but their video doesn't get very many views. However, Team Legacy shows up through a portal. Panda needs the camera, but Ice Bear is too busy taking pictures.
Suddenly, a large ship appears, and the landing port opens up, revealing the Thrownaways, CN characters that only appeared in one episode: Beau from Dexter's Laboratory, Piff from Billy & Mandy, Finkman from Whatever Happened to... Robot Jones?, and their leader -- Julie, from Hi Hi Puffy AmiYumi. Julie explains that they want to gain power over the Tooniverse, but Beau notices Dee Dee and remembers how he used to be in love with her. Julie is enraged with this distraction, and commands a large group of robots to attack Team Legacy. Dexter and Julie have a duel, until she knocks him down and attempts to kill him. But Beau steps in the way, and opens a large portal, sucking in everyone except Dexter, Steven, Shannon, and Panda.
Acquired Characters: Grizzly, Panda, Ice Bear.
Giant Battle: Alexandrite See, Monkey Do
Back at Dexter's Lab, Blossom is left in charge. She talks to the Foster's gang about how to stop the Lich, and suggests that they find Bendy. But no one wants to do it! Bloo criticizes this choice until Blossom explains that Bendy fears his world's destruction just as much as he does.
Just then, Blossom scans something near Mojo Jojo's lab. It turns out that it IS Mojo Jojo, but... larger.
Blossom sends Pearl, Amethyst, and Garnet to fight Mojozilla, in the form of Alexandrite. He wants to capture Blossom, but Alexandrite throws him back into his lab, and he goes back to normal size and rushes into a portal.
Most of the characters fall into another dimension. Due to his interdimensional travels with the Thrownaways, Beau identifies this dimension as Bellwood -- but, a rift is forming there. Gumball sees a green glow, and suddenly recalls a movie he once went to see -- about a teen who used a device known as the Omnitrix to morph into different aliens in combat.
The glow comes closer, revealing Ben Tennyson. He is looking for Vilgax, and believes that Team Legacy knows where he is. But Vilgax has already shown up, and fights them for a while.
After the battle, Team Legacy returns to Dexter's Lab, with new recruits: Ben Tennyson, Beau, Piff, and the Bare Bears. Dexter, having returned via Blossom's portal, introduces himself to Ben. They later search for Peridot in Homeworld, but there is no sign of her.
Acquired Characters: Ben Tennyson, Beau, Piff.
Peridot wakes up in a strange place, and is chained to a wall. Julie enters her prison cell, and orders Finkman to prepare the Mind Sucker; fortunately, Dexter sneaks in and releases Peridot. They fight Julie's robots, alongside the rest of Team Legacy. Peridot realizes that the Gem Warship is heading for Marzipan.
Aboard the Gem Warship, the Lich makes a change of plans, and heads for the land of Ooo.
Nicole, Richard, and Anais are looking for Gumball and Darwin. They come across Kaz and Nergal Jr. along the way, and then Carrie arrives and warns them of the approaching end of existence. But halfway through her message, she freezes in stone. The others rush to the Wattersons' car; Nergal Jr., having a crush on Carrie, places her gently into the trunk. The six of them begin to turn into stone, but they soon find a portal and drive through it.
Acquired Characters: Nicole, Richard, Anais, Kaz, Nergal Jr., Carrie.
The car crashes into Marzipan. The Wattersons reunite, and Ami and Billy hug Kaz and Nergal Jr., respectively. Dexter realizes that the Lich has made a detour, but Doom Forest creatures show up, ready to gobble them up. Team Legacy manages to beat them, and Dexter opens a portal to Ooo -- but not before Chowder joins them.
Acquired Character: Chowder.
Land of Ooo/Centurica
Team Legacy lands in Ooo, where there is no sign of Finn and Jake's tree house or Princess Bubblegum's castle. Dexter leaves Gumball and Billy in the ship -- and specifically tells them not to touch the nearby time machine. But Billy presses the button, not knowing what it does, and he and Gumball end up in Centurica, during the events of Destination Timewarp II: How Did My Evil Clone Come Back From the Dead?!. They come across Julie again, but this time, she appears with a dark empress from another timeline -- Ballgum. Warpverse Princess Morbucks is working with her as well.
The Warpverse counterparts of Dexter, Blossom, Steven, and Finn leap through a time hole to fight Morbucks. But they suddenly notice Gumball and Billy, who must explain that they are on their side. The six of them fight Ballgum, Julie, and Morbucks. Near the end, Beau brings the time machine back, and tells them to get in -- but not before he is captured himself, alongside the Warpverse League.
Gumball and Billy return to their multiverse, only to realize that Blossom has been captured, and there are only two days till the Turner Portal opens up. It turns out that time goes much faster in Centurica than anywhere else. Dexter is enraged with them, and kicks everyone off his ship, saying that he should never have let them help him. But Julie comes to Ooo and kidnaps the rest of Team Legacy; she is now on her own.
Dexter is soon captured as well, and the team is forced to watch "The Heart" -- a.k.a. Virus -- crawl out of the Turner Portal, before they are sucked in. However, Virus betrays Julie and sucks her in as well, along with the competing Lich forces.
The Real World
Julie, Mojo Jojo, anc Cubey are the only ones able to move in the real world. Cubey tries to convince Julie to help them save the heroes, but she runs off, saying that she will never be loved. In fact, it is the boy known as Kyle who gets her to help -- she was his favorite character in Hi Hi Puffy AmiYumi. Kyle drops Team Legacy into the "BACK TO YOUR WORLD" tube.
Acquired Characters: Julie, Mojo Jojo.
Virus is taking over Townsville and its suburban district Huber, and he has captured Professor Utonium, the Mayor, and Miss Bellum. Team Legacy starts to fight him, with the help of the Warpverse League.
Virus severely wounds Tooniverse Dexter with his electricity. Blossom begins to worry for him, and Gumball, Grizzly, Yumi, Moxy, and Finn want to share the last of earth, wind, fire, water, and heart. But Gumball suddenly notices something -- they had just summoned Captain Planet! The latter heals Dexter, and the team is prepared to continue the fight.
Mandy fuses with Virus, the Lich, Yellow Diamond, and Vilgax, forming Forever. Mojo Jojo borrows Dexter's ship, and heads for his volcano lab so he can use one of his secret weapons -- a power outage system. Blossom tosses him the plug, and Forever is separated. However, Ballgum appears and threatens to take the entire Tooniverse for herself. Beau arrives to stop her, opening a portal similar to the Turner Portal, sucking both Ballgum and Virus in. Julie goes in as well, so she can prevent Virus from returning.
All the dimensions are restored, and everyone returns safely home. Dexter feels that Julie didn't deserve to be trapped in the Turner Portal, but Blossom reminds him that she's where she needs to be. He begins to feel better, and invites the Powerpuff Girls over to his house for a big dinner.
At the dinner, Dexter's and Blossom's families, along with Beau, have a good time, knowing that their latest mission was probably one of their greatest...
Acquired Characters: Captain Planet, Warpiverse League (Finn, Dexter, Steven, and Blossom of the Warpiverse)
In the mid-credits scene, a man is reading a newspaper. He tells someone named Harley to prepare the weapons for the destruction of a certain superhero known as Batman.
In the post-credits scene, two abnormally large hands investigate the dimensional disturbances in the Tooniverse. One tells the other to get ready, because he knows they will end up facing a similar threat. He leaves behind a flag showing a white circle with a corner cross on it...