Despite the failure of "Operation Big Wave", Sonic and the rest of the Resistance continue their struggle against Eggman's forces. Their next target is the database found in the Chemical Plant, so Tails and Classic Sonic head out on a mission to hack into the computer systems. While this is going on, Metal Sonic is seen attacking the city, so Sonic and the rookie team up to battle the imposter. Although a fake created by the Phantom Ruby, this version of the robot is even more powerful than the original, but it's still nothing Sonic can't handle.

According to the data Tails finds, the Phantom Ruby is powered by an energy reactor found in the Death Egg. If the Resistance can destroy the floating station, the Ruby will become almost powerless. The heroes split up in a daring series of missions, with the rookie setting off for Green Hill to provide a distraction, while Sonic goes back to Chemical Plant to access the main computer room and remotely disable the Death Egg defenses. Once completed, Classic Sonic alone heads to the space station to do what he does best, bringing Eggman's favorite weapon down once again...