Within the Special Stages, the player must use the stylus of the Nintendo DS in order to move Sonic. Touching Flappers and Egg Bats with the stylus will cause Sonic to jump and perform a Homing Attack on the robots. Balloons also appear in these Stage, only as special trick-combos that Sonic can perform when the player moves the stylus to a series of numbers on the screen in numerically order in a short time limit. If successful, Sonic will earn bonus Rings.
Each Special Stage has two checkpoints, each containing a number of specific Rings for Sonic to collect in the stage. If Sonic collects the exact number or more of the rings by the end of the first segment, he moves on to the second segment of the Special Stage. The same thing goes for when he collects enough rings in the second segment, only he gets a Chaos Emerald at the end of each Special Stage if Sonic makes it through both segments.
The Zone the player enters the Special Stage will determine the color of the Chaos Emerald Sonic earns, unlike in past Sonic games, namely Sonic the Hedgehog 2, where Sonic went to the next Special Stage for the next Emerald regardless of which Zone. In these Special Stages, Sonic will continually earn the same colored Chaos Emerald if he enters a Special Stage of the same Zone. Here is a list of zones where Sonic can reach the specific Chaos Emerald: