Dr. Eggman, seeking a power source as potent as the Chaos Emeralds, has developed a new machine to locate such crystals. His search has led him to Blossom Island, a Japanese-inspired archipelago. Eggman intends to exploit the island's resources, including the newfound crystal. His scheme also involves the introduction of new villains, Bark and possibly Bean.

Sonic, Tails, and two new characters must unite to thwart Eggman's plans and prevent him from harnessing the power of the new crystal.