Sonic, Ray and Mighty have been kidnapped by the evil Doctor Ivo "Eggman" Robotnik, who uses his large tank vehicle to do so. He takes them prisoners on Eggman Island: an island littered with traps and hazards that can be activated with the push of a button.
Sonic, Ray and Mighty team up to escape the island, as the trio must survive the various hazards of the island and reach Eggman's Tower. As they arrive at the control room, Eggman presses a button that triggers a self-destruct sequence that will destroy the entire island. The trio manage to flee the island before the explosion. The evil doctor also escapes, but suddenly falls into the sea due to his Egg Mobile running out of fuel.