- For Special Stages in general, see here. For the Wii version's Special Stage-like levels, see Game Land.
The Special Stages in the Nintendo DS version of Sonic Colors are a series of special levels. While the levels resemble the half-pipe courses used in Sonic Rush, they have a different gameplay style but the player is rewarded with a Chaos Emerald for completing the level. When all Chaos Emeralds are collected, the player unlocks the secret final boss, Nega-Mother Wisp. (Unlike the Wii version, the player cannot use Super Sonic in the regular stages.)
To access a Special Stage, the player must have finished any regular stage with at least fifty Rings. Once the score is calculated and the player is ranked according to the score, the player is given the option to enter the Special Stage.
Like in the Special Stages of Sonic Rush, the player controls Sonic using the stylus. The objective is to collect a certain number of orbs of a certain color in three sections: in the first section, the player has to collect a number of red glowing orbs while in the second section the player must collect a number of blue glowing orbs and in the third and final section, a certain number of yellow orbs must be collected to finally finish the stage with a Chaos Emerald. While guiding through the stage, the player must be careful not to collect the wrong-colored orbs although they won't take any spheres off Sonic, the player may not have enough orbs of the next color to proceed. There are multi-colored orbs which are worth five of any spheres.
- The music that plays in the Special Stages of Sonic Colors is a remix of the "Battle: City Area" music from Sonic Heroes.