The first chapter consists of four Zone levels, each with three Acts, including two normal Acts and one Boss level. Unlike earlier generations, however, the game includes a world map, so players can play through the map and select any Act in any Zone at will, gradually unlocking new zones as they progress. Only after completing all areas will the player be able to access the final level. The game also features Special Stages, which are similar to traditional Sonic games and are unlocked by collecting 50 rings. The hidden levels follow the same pattern as the initial Sonic, where the player needs to shake the screen and control the level itself to get Sonic through and collect all the rings in order to get a Chaos Emerald. Once all 7 emeralds have been collected, Sonic can transform into his super form on any level. At the end of the game, Metal Sonic's shadow appears on the screen, along with the words "To Be Continued".

The next chapter uses 5 levels and the backstory is a sequel to Sonic CD, where Eggman hatches a new evil plan and awakens the long-sleeping Metal Sonic, but Metal Sonic seeks out a treasure with powerful energy and becomes so powerful after absorbing it. After seeing a transport rocket on a hill and also seeing Sonic and Tails on a plane, Metal Sonic is enraged and embarks on a mission of revenge with the rocket on board.Sonic and Tails meet Metal Sonic in Winter Park and Sonic once again confronts Metal Sonic. However, after the air fortress is destroyed, Eggman escapes in a capsule, and Sonic and Tails do the same, chasing Eggman, who unfortunately transforms the tiny planet into Death Egg Mk.2. In the end, Sonic defeats Metal Sonic again, and Eggman shows off his ultimate weapon, the Egg Heart. After Egg Heart is destroyed and Death Egg Mk.2 is about to explode, Sonic and Tails escape from Death Egg Mk.2 in a capsule silo and the tiny planet can no longer be saved as it was. ......