Repairs on the Death Egg are finally complete. All that is needed now is a power source, and Robotnik, his sights set on the Master Emerald, dispatches a Badnik to retrieve it. Meanwhile, Sonic and Knuckles have found their way to the volcanic Lava Reef Zone under the Launch Base Zone, the Death Egg sitting right on top of the volcano. Suddenly, they are attacked by a massive army of EggRobos, one of them being used by Robotnik to speak to the heroes directly. Knuckles breaks a wall down, drowning the Eggrobos in molten lava, and leads Sonic to the nearby Emerald Chamber, where his worst fear has been confirmed: The Master Emerald is gone, and without it, the Floating Island will fall to Mobius in just a few hours. Their questions about where it's gone however are answered by a glow from another end of the chamber. The Emerald is there, and drawing power from it is a new Metallix.
Metallix makes his way into a Teleporter with the Emerald, and Sonic and Knuckles follow, arriving in the Sky Sanctuary Zone. The robot draws more power from the Emerald and charges into Knuckles, knocking the Echidna out cold before turning its attention on Sonic. The Metallix reveals that it seeks revenge for the loss of its brother, just one of an elite Brotherhood, and when Sonic tries running circles around it, it stops him in his tracks and tosses him aside like a ragdoll. Down to 15% power, Metallix hurries back to the Master Emerald for a recharge. Sonic gets there first, however, and the Metallix soon finds itself being torn apart as Super Sonic enters the battle. Meanwhile on the Death Egg, Robotnik is enraged at having lost Metallix, but fortunately for him, the robot left the Master Emerald on the teleporter. Back in the Sky Sanctuary, Knuckles comes around just in time to see Metallix's head go flying but is soon being violently attacked by Super Sonic. Luckily, Sonic doesn't stay Super for long, and turns back to normal before he could seriously hurt Knuckles. Too late, they realise that the Master Emerald is gone, and the Sky Sanctuary is beginning to crumble. Before they can get on the teleporter, they hear a loud rumble like thunder. Something big is coming their way....