The story opens with Mario and Kirby fighting on a stadium that is located in the Smash Bros. world. A purple cloud slowly forms around the stadium, where the Ancient Minister and his Subspace Army appear and detonate a Subspace Bomb, transporting the stadium into Subspace. As the Ancient Minister's armies spread across the land, some heroic characters team up and attempt to repel the enemy, while a number of villainous characters compete to harvest the power of the allied characters by converting them into rock....
It is revealed that the Ancient Minister is subordinate to Ganondorf, who is under orders from Master Hand to draw the world into Subspace. The Ancient Minister's true identity is found to be that of the Master R.O.B. unit, and he eventually rebels against his superiors and joins the allied characters. The allied heroes enter Subspace, where it is revealed that R.O.B., Ganondorf, and even Master Hand were all being controlled and manipulated by an even higher being, Tabuu. Tabuu unleashes a power blast which transforms all of the protagonists into Rock, but a select few are revived by brooches that were attached to them by King Dedede earlier in the story. They work together to revive the other characters scattered across Subspace and make their way through a great maze with Tabuu waiting in the center. Following an ambush conducted by Sonic the Hedgehog and Mario, the allied characters ultimately defeat Tabuu, saving the Smash Bros. universe.
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