- For Special Stages in general, see here.
Completing a Special stage will grant the player a Chaos Emerald and if the player has all seven Chaos Emeralds (by completing all seven Special Stages), the player will be able to access the game's true final level, The Moon Zone, as Sonic after he clears X Zone. Note that the Emeralds are shared, so any character can collect any Chaos Emerald.
For one to access a Special Stage, the player needs to find a Special Spring hidden throughout the following stages. Each of the location's springs will lead to their corresponding Special Stage:
- Neo Green Hill Zone Act 1 (Special Stage 1)
- Secret Base Zone Act 2 (Special Stage 2)
- Casino Paradise Zone Act 1 (Special Stage 3)
- Ice Mountain Zone Act 1 (Special Stage 4)
- Ice Mountain Zone Act 2 (Special Stage 5)
- Angel Island Zone Act 2 (Special Stage 6)
- Cosmic Angel Zone (Special Stage 7)
These springs will launch the character up into outer space, where they get on a board and traverse through a bottomless hole. During the fall, the character will need to collect a certain number of Rings in order to pass through two segments; otherwise the player will fail the opportunity to clear the Special Stage and earn the Emerald. Along the way, the player also needs to avoid bombs which take away ten Rings from the player's total. The player can press to make the character perform a trick on a board which is essential to collect Rings or avoid obstacles. There is also a giant yellow round void that if the player presses at the right time, the player will earn additional rings. There are also Bumpers that catapult the player backwards (hold when hitting them to bounce backwards further) and Springs that catapult the player forwards in a given direction (the player will not be able to control their character while being catapulted). Finally, there are also a Chao in each Special Stage that the player can tag to earn a Continue.
The Special Spring can only be used once per visit to an Act, so if the player fails to get the Chaos Emerald from the Special Stage, they will not be able to return back to the Special Stage again in the same visit unless they lose a life or restart the game from the beginning of the Act. Upon exiting a Special Stage, the player will spawn next to the Special Spring they used and can continue from where they left off.
- The boards the character rides on in the Special Stages somewhat resemble Extreme Gear from the Sonic Riders series games although the said series debuted a few years after Sonic Advance.