It's another drull day when Peach confronts Mario about the disappearance of Bowser. While normally a good thing, Peach is worried that this may lead to some other danger because of his absence. Mario and Luigi decide to help investigate the matter, following Peach on another adventure, unaware that they are about to confront an enemy more dangerous than ever before.

Set a good while after the main Sonic series, a new evil awakens and begins to take shape. This calls for a new band of heroes, but they are coming up against a force far beyond anything they were expecting...