In Sonic Chaos (also known as "Sonic & Tails" in Japan) for the Game Gear and Master System, Sonic and Tails were facing the threat of Dr. Robotnik sinking South Island by improperly using the Chaos Emeralds. Sonic and Tails collected the Emeralds before the doctor could, including the red one he already had in his possession and liberated the island of his control once more.

Spinball Time:
In the spin-off Sonic Spinball, Sonic went to Mt. Mobius, which was taken over by Dr. Robotnik and made into his "Veg-o-Fortress". However, Sonic was knocked off of Tails' airplane on the way, causing him to travel through Mt. Mobius in a pinball styled way from bottom to top. On his adventure to the top, he collected Sixteen Chaos Emeralds and rescued Tails, along with characters from the Saturday Morning TV Series: Sally Acorn, Bunnie Rabbot and Rotor Walrus.

In the end, Sonic defeated the doctor and his Veg-o-Fortress was destroyed while the speedy hedgehog made his escape together with Tails and his airplane.