A year has passed since the six Chaos Emeralds were restored to South Island. With the Emeralds being kept in the island's North Cave, peace reigned over South Island, with the exception of Sonic and Tails kept themselves busy with loud practice runs. One day however, while Sonic and Miles "Tails" Prower were gone on an adventure, Dr. Robotnik managed to procure one of the Chaos Emeralds to create nuclear bombs and laser weapons from the North Cave. As a result, the rest of the Emeralds scattered around the island and, without the Emeralds' power, South Island begins sinking into the sea. Hearing rumors of Robotnik's plot, Sonic and Tails returned to South Island, only to find it in chaos. With no time to lose, the duo rushed off to stop the mad doctor's plan and save the island by regaining the Emeralds.
—The Super Blackwing