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The story starts at Finn's Treehouse, where Mario and Peach where paying a visit to. Mario, Peach, Finn, and Jake are simply hanging out when the door to the treehouse crashes open! An army of elves are storming the Treehouse, commanded by the Ice King. Jake escorts Peach out of the Treehouse while Mario and Finn fight the Ice King and his elves. After defeating the Ice King, Mario and Finn escape the Treehouse and decide to head to Princess Bubblegum's castle.
Green Hill Zone
Silver is at Green Hill Zone when an Elf Army attacks, hoping to defeat Silver so that he doesn't interfere with the plan like he did last time. Silver tries to hold off the Elves but is turned into a trophy. However, Nabbit jumps by and takes the trophy for himself.
An army of Elves are invading Skyworld, led by Medusa, and Pit is rushing to warn Palutena and the other deities, before being surrounded by an army of Elves. However, one of the elves transforms into Amethyst and she, along with Steven, help Pit take down the Elves. Medusa fights the team, and defeats Amethyst, taking her trophy. She then reveals that she has the trophy of Palutena as well, and runs away. Pit and Steven then defeat the remaining elf minions before chasing after Medusa and the trophies.
Death City I
Maka and Soul are travelling through Death City before getting a transmission from Shinigami, saying that a "witch" is attacking the city. Soul turns into his scythe form as he and Maka take down Elf minions before finding out that the witch is, in fact, Medusa, who tries to turn Maka into a trophy when Death the Kid jumps out and blasts her. The two chase after Medusa and meet up with Pit and Steven.
Barney is attacking the Comet Observatory, using his imagination to create many deadly weapons. Rosalina and Ruby Rose try to stop him, but to no avail.
Meanwhile, Mario and Finn are mysteriously teleported into Barney's Mind. While inside Barney's mind, the duo try to prevent Barney from imagining any more weapons, making Rosalina and Ruby Rose beat him more easily. After Barney is defeated, Mario and Finn are teleported out of Barney's mind and meet up with Rosalina and Ruby Rose.
Nostalgia Critic's House
Meanwhile, at the Nostalgia Critic's house, the Nostalgia Critic is finished making a review of Don Lockwood's newest movie and sequel to Singing in the Rain, titled Dancing in the Hail. Don sees the review and is angered about how absurd he thinks it is. Don goes to the Critic's house and they begin to have an argument, when suddenly AVGN attacks the Critic and they have their usual skirmish. After the battle, the three are attacked by a brainwashed Todd in the Shadows. Don, the Critic, and AVGN chase Todd back to his house, where he plays a strange tune on his piano. After playing the tune, a wormhole opens up and it swallows Don, Todd, The Critic, and AVGN.
Don, The Critic, and AVGN exit the Wormhole along with Todd, who is no longer brainwashed. They find themselves in the Underworld, and find out that Hades was the one sending the Elven soldiers. He sends Medusa to attack the four, but the team defeats her and revives the trophy of Amethyst. The team now fights Hades' underworld soldiers, led by Dark Pit. After defeating Dark Pit, the team charges at Hades, but instead are sent through another wormhole.
BlackStar is on Rainbow Road, likely on another epic quest to show himself off when he comes across Mario, Finn, Rosalina and Ruby Rose. BlackStar agrees to help them, despite planning to take all the glory for himself, but suddenly Hades' underworld army attacks. The team defeats the underworld army but just when the heroes seem to get the upper hand, the army's numbers increase! Suddenly, Rocket Raccoon jumps in and blasts them all with his guns. The team continues to traverse the cosmos, while one of Hades' spies is watching them.
Death City II
Maka, and Death the Kid are patrolling Death City when Nabbit comes in and fights the two. After winning they revive Nabbit's trophy, and Nabbit reveals he is actually a double agent for the Megald Warriors, and he revives Silver's trophy.
Later on, they find Demon Alpha and face him. Silver is initially confused as to why he is here, but comes to the conclusion that he came from a timeline where Alpha remained under the Forbidden Power's control. Suddenly, flaming barriers surround all of Death City, and Hades' voice is heard, mocking the Megald Warriors and stating that he has taken the city hostage.
Comet Observatory I
Mario and co. arrive at the Comet Observatory, where they find Eren Jaeger, Princess Peach, and Jake the Dog. Jake states that they've been researching the strange happenings in Megald. Hades has apparently been using Dark Matter to open portals to other timelines. Suddenly, a Dark Matter Portal is opened and out come Corrupted versions of the Megald Warriors from other timelines. BlackStar and Ruby fall into one of the portals, while the remaining Warriors fight off their corrupted copies.
Ruby and Blackstar are in a world known as Timeline S, where all the citizens of Megald are corrupted by Hades' power. Hades has killed the two major gods and has brainwashed everyone. They face corrupted versions of Rukio Matoi, Proto Man, and Cucumber. After defeating the three, the two bring them back to their normal state. Ruby notes that the three are absent in their timeline, and decide to take them with as they try to escape Timeline S.
Meanwhile The Critic's team has also found themselves in Timeline S. They face the brainwashed versions of themselves and find a portal that leads to Death City. Ruby, Rukio, BlackStar, Proto Man, and Cucumber meet up with them and all together they go into the portal.