Gameplay takes place between two parallel storylines; the player has the option of advancing in either one or the other at any time. The "Hero" story featuring Sonic, Knuckles, Tails and the non-playable Amy, while the "Dark" story featuring Shadow, Rouge (she isn't really dark: she is a secret agent for the president, and she is on a mission ), and Dr. Eggman play similar to each other, with each hero character playing similar to the respective dark character. Levels advance in order for each storyline, alternating between each of the playable characters.

Levels featuring Sonic or Shadow are designed much the same as they were in Sonic Adventure,[1] wherein the player's primary objective is simply to get to the end of the level. Levels with Tails or Dr. Eggman allow the player to control a mechanized robot walker and generally blast their way through to the end of the stage. Knuckles and Rouge are required to scour their levels for shards of the master emerald. Interspersed between the levels are various bosses, which one particular character must fight.

At the end of each stage the player is given a score and rank based on performance. Similar to school grades, you're ranked with a grade of A, B, C, D, or E (with A being the highest and E being the lowest).