The Special Stage in the Nintendo 3DS version of Sonic Generations uses the same concept as the Sonic Heroes Special Stage, where Modern Sonic runs through a half-pipe and collects spheres scattered along the pipes while dodging bombs. Each Special Stage is unlocked after clearing both Acts of each level, and all of them must be completed in order to complete the game.
The rules of the Special Stage are based off the source material's Emerald Challenges, but with the music from the Bonus Challenges; the Chaos Emerald is floating towards the end, and the goal of the stage is to catch up to the Emerald before it reaches the end of the stage. To do this, the player must collect spheres to build up boost power and Boost after the Emerald with , while dodging obstacles such as bombs and electric gates that will knock them down, allowing the Emerald to distance itself from them. Later stages have Dash Panels that make Sonic go into a rolling state, and even Springs that will send the player through a series of Dash Rings.
Unlike the regular stages, Sonic's boost gauge displays a timer that counts how long the player maintains the boost, resetting to zero should the player stop boosting. In addition to regular spheres, the star-patterned Power Spheres that refill greater amounts of boost power return, along with the introduction of glowing Rainbow Spheres that will completely refill the gauge should Sonic grab only one of them.
The main differences between this iteration of the Special Stage and the one in Sonic Heroes is that Sonic is the only character, and as such Formation Change Gates are nowhere to be seen. The controls are also much smoother compared to Sonic Heroes, making the Special Stage far easier to complete.
List of stages