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Mario's archenemy Bowser joins forces with Sonic's archenemy Eggman, and they decide that if they can't defeat their respective enemy, perhaps the other can. They also plan on unleashing an ancient evil to take over all of the worlds. Mario is sucked into a vortex, and encounters Sonic the Hedgehog, but they are soon in the opposite worlds. Mario battles and defeats Eggman in one of his machines, and Eggman flees. Mario goes after Eggman to find a way home with the aid of Sonic's friends.
End: Mario defeats Eggman, and is sent to a nexus outside of all worlds where he meets up with Sonic. They work together to battle the Dark, the ancient evil that Bowser and Eggman released. After defeating the Dark, Mario and Sonic go their separate ways.
Sonic was lounging doing his ordinary things when he is sucked into a vortex and encounters Mario, but Sonic is soon in the Mushroom Kingdom. Sonic has a battle with Bowser, but Bowser flees. Sonic goes after Bowser to get back to his own world with the help of Mario's friends.
End: Sonic defeats Bowser in his castle, and winds up in a nexus ouside of worlds. Alongside Mario he fights the Dark, and they win. After their victory they part ways, and go back to their own worlds.
The Dark is revealed to have survived the battle in Super Smash Bros. Battle.