The story opens after Sonic Adventure 2. Sonic and his friends had finally put an end to Dr.Robotnik's schemes and saved the world from total annihilation from the menacing Bio-lizard, the first ultimate lifeform. But sadly at the cost of Shadow the hedgehog's life, who had finally fulfilled his promise to his long lost friend, Maria, to bring peace to planet earth. The heroes are now getting the rest they deserve, awaiting their next adventure into the unknown.
The blue blur was running through green hill zone while reminiscing about the final battle upon the ARK as he mumbles the words of his fallen ally, Shadow, that had stuck to him for the past few weeks. "The ultimate lifeform might be you. What did he mean by that?" Sonic leaps onto the platform of the loopty loop as he stares off into the star-lit night. Sonic's ear twitches as he hears a familiar voice call his name. It's his friend Tails. Sonic waves with a gentle smile that soon fades back to a look of sorrow. Tails flies down to the platform as he slowly sits down next to sonic. "Sonic, are you doing okay? You usually have that witty smile on your face." "It's nothing tails." Sonic replies with an upset tone in his voice. Sonic lets out a disheartening sigh. "I've been thinking about what shadow said to me during our fight with the Bio-lizard. He told me that I may be the true ultimate lifeform. What do you think of all this, Tails?" Tails starts to think about it all as he walks back and forth mumbling Sonic's words to himself. Suddenly a spark lights within his mind. "Wait, I think I remember something while reading Dr.Gerald Robotnik's diary," he says with a curious tone. "There was something in his book about the chaos emeralds and how they're connected to something not of our world. I think he called it the chaos force."