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Mecha Madness is the story mode of Eternal Brawl Uprising. It focuses on the heroes uniting once again to stop Eggman's Empire.
In the Eternal Tournament, many fighters have came together to celebrate the defeat of the God Loki. In the first match, Mario is fighting Sonic. After the battle, the winner revives the loser, yada yada yada, but then, a fleet of airships swarm in. Mario and Sonic get ready to fight, but a trophy gun is fired and nearly hits Sonic, who gets out of the way just in time. Soon, an army of Badniks come down and attack the two. However, Ruby Rose and Megaman bust in and help defeat them. After defeating the Badniks, the four see a metal replica of Loki. After defeating the replica, Loki reveals that he has a Subspace Bomb hidden within him. The bomb is activated, and Sonic is sucked in. Mario, Ruby Rose, and Megaman escape to warn the others.
Bowser is in Koopa Castle, when suddenly he hears a loud noise. Lucario is storming the castle, and Bowser sends Koopa to defeat him. Lucario defeats Koopa, and attacks Bowser. Bowser defeats Lucario, and discovers that the entire castle is filled with Pokemon. Serena comes in and uses her Pokemon to defeat Bowser, and then revives Lucario. Serena and Lucario decide to escape the Koopa Castle before they are caught by the Koopa Troop.
Hatsune Miku is getting ready to record a new song when Herobrine busts in with an army of badniks. Miku defeats the badniks and gets ready to face Herobrine, but Herobrine hacks into Hatsune Miku's data and deletes her voice program, preventing her from using her singing abilities. Hatsune Miku chases after Herobrine, but Herobrine jumps into a portal, with Hatsune Miku following.
Dexter is at the Town Square, on his way home to test out his latest invention, when he hears a loud rumbling, and a Charizard attacks. After defeating him, Dexter tries to tame the Charizard when Mario, Ruby Rose, and Megaman come in. Mario explains that they need Dexter's help to stop Doctor Eggman. Dexter agrees and the groups rides Charizard towards Dexter's home.
Hatsune Miku jumps through the portal and ends up in ;Lavendera, where Alpha and Flamegirl see her and think she's a hacker. After defeating the two, Hatsune Miku revives them when Herobrine attacks. They defeat Herobrine, with Miku getting her voice restored, but Metal Sonic dives in and turns Flamegirl into a trophy. Metal Sonic dashes out with the Herobrine and Flamegirl trophies, with Hatsune Miku and Alpha right on his tail.
The Mystery Shack
Dipper and Mabel are trying to solve another mystery when suddenly a portal opens. Sonic jumps out of the portal, and he seems to have been corrupted by Dark Matter. Dipper and Mabel fight Sonic and restore him to his normal state. Soon, more Dark Matter and Badniks come out of the portal. Dipper, Mabel and Sonic fight them, but soon get sucked into the portal themselves.
Mario, Dexter, Charizard, Ruby, and Megaman enter Dexter's Lab, however it seems that all of Dexter's machines have been reprogrammed by Dr. Wily. After defeating the robots. They face Dr. Wily in his newest mech. Soon Dr. Wily is defeated, and reveals that he has teamed up with Dr. Eggman to control the Eterniverse before he is teleported away.
Serena and Lucario exit Bowser's Castle and avoid the Koopa Troop, before running into ERod and The Nostalgia Critic. Not knowing what's going on, ERod and The Nostalgia Critic fight the two, ending in ERod and The Nostalgia Critic becoming trophies. Suddenly, Metal Sonic flies in, and steals The Nostalgia Critic's trophy. Serena and Lucario revive ERod and chase Metal Sonic through a portal.