In Sonic Chronicles: The Dark Brotherhood, a mysterious force has begun to tear apart the world and Sonic and his band of friends (11 of them playable) must come together to fight off the menace and bring peace back.

The gameplay is a mix of action and RPG where players explore a map, collecting items and rings, which can be used to buy new special attacks and solve puzzles that are unique to each of the characters in the players party. To fight the player customizes their party of four from the eleven playable characters and uses the stylus to rhythmically tap and drag at a precise time to complete attacks and string together a group of deadly combos.

There are 20 different areas to explore, ranging from classic Sonic backdrops to new ones created for the game. Another feature is the "Story So Far Feature", which does a quick recap of the players progress each time they start their game back up.

Players can also go wireless through Wi-Fi and trade Chao, a unique artificial life form, each with their own distinct power-ups and abilities that can be used in battles.