In a laval planet, similar like the planet of the final battle of Star Wars III - Return of the Sith. The S.S Toonami reaches the planet, and TOM descends from the S.S Toonami. In the greatest building of the planet, The Lich, Garret Bobby Ferguson Jr., Father, Yellow Diamond, Blue Diamond, Mojo Jojo, Demongo, Future Mandark, The ACME president, The Big Boogey and Captain Pollution were in the Evil Office. They leader, Aku, appeared and sended the Lich to kill TOM, you need to fight The Lich using TOM, however, at the end the Lich nearly kills him, but two robots carried TOM to the S.S Toonami, and the S.S Toonami leaves the planet.
After awakening, TOM uses a computer to locate the greatest heroes of the Cartoonverse.
Rush on the Lab
Dexter was inventing a portal to travel trough dimensions, but Dee Dee appears and press the button that actives the portal, TOM jumped to the portal and kidnapped Dexter using a potato empty bag. However, Dexter scapes easily and actives all his robots to attack TOM, but all the robots became evil. You control TOM and Dexter, after defeating all the robots, a giant robot scaped of the lab.
Dee Dee was trapped in a cell by Dexter to protect her, and the robot began to destroy the Lab, but Dexter and TOM destroyed the robot, Dee Dee scaped of the cell and pressed a button, and the robot exploded, TOM telled that Dexter that a lot of deadly villains assembled, and TOM wants to reunite the greatest heroes to stop them.
Return of the Lich
Finn and Jake were in Ooo playing videogames and the Ice King was in his castle with Gunter, but a black nible covered all the screen and The Lich appeared, The Lich burned the Ice King's castle and flied to Finn and Jake's treehouse, the threehouse was destroyed by The Lich, you control Finn and Jake to defeat the Lich, but The Lich scaped destroying parts of Ooo, but TOM and Dexter appeared and they talked to Finn and Jake about all.
After reaching the Lich, he took Jake and launched him to a portal, Finn, Dexter andTOM jumped to the portal and The Lich scaped by a dimensional rupture. TOM, Finn, Dexter and Jake were travelling to a dimensional tube and ended in The Park.
Portals in the Park
TOM, Dexter, Finn and Jake appeared in the Park, but many red portals appeared in the Park, and a lot of enemies approached the group. After defeating all the enemies, the group entered to the House of the Park and Mordecai and Rigby were playing videogames, Benson said the two 'Return to the Job!' And he was absorbed by a portal, the group encountered Mordecai and Rigby and they talked with both,
The group were in the dimensional tube, but many Adventure Time, Steven Universe and Dexter's Lab appeared, but Benson suddenly appeared, but an evil robot kidnapped Benson, after defeating the rest of the enemies, the robot scaped with Benson to another dimensional tube.
Beach City Invaded
In the Steven Universe dimension, Steven and the Gems were fighting in the beach a lot of enemies that emerged from many red portals, you control Steven and the Gems, suddenly, Lapis and Peridot (into her Peri-Mech) defeated the enemies, a portal appeared and the group arrived into Beach City, however, Demongo appears and summons a lot of portals...but of one portal jumped...Samurai Jack!
You controll Jack, you need to defeat Demongo and help the Gems and the group to stop the enemies, Samurai Jack jumped to the portal and a red laser fell to Demongo, disappearing him, the group and the Gems and Steven entered to a portal...but Dexter and Samurai Jack jumped to another portal.
It was a 'normal' day in Townsville, the Powerpuff Girls were awakened by Professor Utonium, but Bubble's octopus plush disappeared! Bubbles began to cry, but her toy floated in the window, Bubbles ran excited to the backyard, but a hand took her. The group arrived in Townsville and the Girls saved Bubbles. TOM convinced the girls to join to their squad to stop the evil, but from the portal, Father (from KND) jumped and tried to kill the Squad, The Lich appeared trying to kill TOM again, but The Lich and Father jumped the one to the other, fusion into Father Lich (or Benedict Lich).
But Mojo Zilla scaped of his tower destroying all, he summons a lot of enemies, but after defeating the enemies, you must defeat Mojo Zilla and he turned into his normal form (Mojo Jojo), Mojo Jojo scaped from a portal, but Father Lich jumped to a red portal.
In The Amazing World of Gumball dimension, Gumball, Darwin and Anais awakened to go to school, in the Elmore High School, there is a party because the 200th Aniversary of the Foundation of the city, however, Father Lich appeared of a portal making purple portals everywhere, enemies invaded Elmore and Gumball and Darwin where turned into trophies with the actual CN logo in the base, however, Samurai Jack and Dexter rescued them, you must defeat Father Lich and the enemies.
After defeating Father Lich, he explodes into a Lich trophy and a Father trophy, and a giant black hole absorbed Elmore. The squad got late, Finn, Jake, TOM, Steven, The Powerpuff Girls, The Crystal Gems, Dexter, Samurai Jack, Gumball, Darwin, Mordecai and Rigby appeared in the dark planet in the Elmore School full of enemies. The trophies of Father and Lich appeared on the Evil Tower, and Aku sended the Diamond Autorithy to the Sector V.
In the KND: Kids Next Door dimension, the Sector V members were on a water submarine. Numbuh 362 sended them to stop a 'Chainsaw Cracken' the Chansaw Cracken was about to dig a hole in the submarine, but Numbuh One jumped in a water suit and used a laser cannon to melt the Chainsaw Cracken's head. A nuke bomb was diving in the water, but all the members of the Sector V launched the nuke bomb with the Cannon to the Ocean Abyss.
After returning to the surface, the kids had seen that the Sector V and it city were conquered by Yellow Diamond and Blue Diamond, all the citizens were slaves and the Moon Base was turned into the New Command Center, Numbuh One found Blue Diamond and tried to kill her, but Blue Diamond shot a powerful blast to Nigel, and he was turned into a trophy and captured, however, the Squad appeared and fought Yellow Diamond, defeating her....the Diamonds scaped to the Evil Planet in a Spider-Robot, but the city was devoured by a black hole.
Nigel awoke on a futurist dark city, it was the Aku City, that was on Aku's control. From a portal, Princess Flame, Samurai Jack, Ben Tennyson, Generator Rex, Ami, Yumi, Mac and Blue appeared. Suddenly, Demongo tried to kill Nigel with a fire shot, however, Princess Flame fought Demongo with the help of Nigel and Samurai Jack. After a long fight, Demongo scaped and flied away.
The team ran following Demongo, however, they were so slow, but Uncle Grandpa appeared on the Realistic Giant Flying Tiger to help them. After entering on Aku's Castle and defeating his guards, Demongo appeared and shot a fireball sending down the group.
After a second battle with Demongo, Aku fought them, after a long battle, Aku was about to die, however, when Samurai Jack was preparing the final attack, Demongo stepped in front of Aku receiving the sword slash. Demongo (as a ghost) ordered Aku to take his soul, so Aku finally ate Demongo's soul, increasing his power, Aku created a huge explosion with only one attack launching away the group.
Meanwhile, in Polyneux School, Robot Jones was in the yard, however, he was attacked by an army of dark copies of all the playable characters of the game leadered by a dark copy of himself. Suddenly, a portal with Billy, Mandy, Grim Reaper, Clarence, the Bears, Wirt, Greg and Ash Ketchum appeared. They talked about the way they ended in Polyneux, and alongside Robot Jones, they fought the dark clones.
Before they were trapped by the clones, the Squad 01 appeared and with the help of the newcomers, they defeated the dark clones, another portal appeared driving the group into an abandoned spaceship.
All the group was transported into the Gem Warship, the Squad (alongside the newcomers and, Peridot, Ice King and the Eds), they found all the villains commanded by Vilgax and Yellow Diamond, but the Squad was captured, however, not all the hopes where dead. Captain Planet appeared and used the elemental power to destroy the Gem Warship Prison Cells.
After scaping, all the villains appeared and after a long battle, the heroes won but they were intercepted by Aku, Vilgax, The Lich and the Diamonds, the main commanders of the Chaos Empire, Vilgax absorbed their souls turning into Fuse-Alien, however, a mysterious portal appeared, and Bugs Bunny jumped out from it and attacked Fuse-Alien.
After a battle with Fuse-Alien, the heroes won separating all the villains, Bugs Bunny drew another portal that led the heroes to Townsville leaving all the villains in the Gem Warship that was about to be destroyed.
The group ended on Foster's Home for Imaginary Friends, Finn told the group that they should return to their worlds, at the end, everyone leaved the stage and returned to their respective dimensions (except Mac and Blue, since they live in that dimension). When no one was looking, Finn, Dexter and TOM talked about the destiny of villains and TOM promised Finn and Dexter that, when a new threat arrived on CN-Multiverse, the Squad would unite again before appearing the credits scene.
After the credits, a text will appear on the screen that says "THE END...OR NO?" returning the game to the Main Menu, unlocking another Story Mode.