Following on from the events of Sonic Heroes, the amnesiac Shadow is struggling to remember who he is and make sense of the image in his head of a young woman named Maria being killed. Without warning, darkness falls upon Westopolis and hundreds of aliens fall from the sky causing havoc wherever they go. Just as Shadow is about to leave, the aliens' leader appears before him. "Shadow, as you can see, the day of reckoning is almost here. Find the seven Chaos Emeralds and bring them to me as promised." Reasoning that finding the Emeralds is the key to unlocking his tangled memories, Shadow sets forth to find out who he really is.