In Sonic the Hedgehog CD, Metal Sonic had been defeated, but survived, albeit was severely damaged, and was left on Little Planet when it disappeared at the end of the game. Dr. Eggman locates and repairs Metal Sonic. Sonic hears that Eggman is back, and reunites with Tails in order to stop him together. Meanwhile, Metal Sonic searches for the heroes and sees them fly away in the Tornado, and follows them using Tails' rocket.
Little Planet makes it's annual return to earth, and it is revealed that Eggman plans to construct a new Death Egg II over the dwarfed planet to power it. As Little Planet heads back into space, Sonic and Tails follow the villains to the Death Egg II. Inside, they confront and defeat Metal Sonic one last time. Finally, they defeat Eggman at the heart of the base. Sonic and Tails then escape in space pods. The duo then head back to earth and while the Death Egg II is not completely destroyed, it has powered down due to the internal damage suffered.
If both episodes are owned on the same platform, Episode Metal can be accessed, which depicts what happened to Metal Sonic in between the two episodes.