Sonic and Tails arrive on Angel Island just as the Hard Boiled Heavies excavate the source of the signal, a mysterious gemstone known as the "Phantom Ruby", from the ground. As they do so, space-time suddenly warps around them, with the heroic duo, the robots, and Knuckles the Echidna, who was relaxing nearby, getting caught in the warp. The group gets catapulted to Green Hill, where it is revealed that the Phantom Ruby's power has transformed the Hard Boiled Heavies into more powerful Egg-Robos and granted them free will. 

As the Heavies rush to get away from the three, Sonic, Tails and Knuckles join forces to stop them. However, they are too late to prevent Eggman from stealing the gemstone from his now-rebellious robots, which he promptly uses to send the heroes to Chemical Plant. Not set back by this, Sonic and his friends continue to pursue the doctor to keep him from using the gemstone's power for evil, clashing with him, the members of the Hard Boiled Heavies, and various other robots, along the way.