The game begins with Doctor Eggman turning Tails, Amy Rose, Rouge, and the Master Emerald into cards with his new device. Sonic and Knuckles arrive on the scene, and find out what has happened. Knuckles, bent on saving the Master Emerald, tells Sonic that teamwork is out of the question and that he needs to get to Eggman first. Sonic snickers and says that he likes a good challenge.

Meanwhile, Shadow the Hedgehog receives a distress signal from Eggman. Suddenly, a mysterious hedgehog named Silver appears from the future. Silver is then pursued by Shadow. When they encounter each other, Silver tells Shadow he needs to get to Eggman, first. After numerous conflicts, it is revealed that Dr. Eggman is in fact Eggman Nega and that the real Doctor Eggman is captured into a card prior to the story. After one final battle with Sonic, Knuckles, Shadow and Silver, Nega is defeated, everyone is reverted to their original forms, and Silver returns to the future with Eggman Nega who is trapped inside a card.