The citizens of Mobius just can't seem to catch a break. Dr. Robotnik (AKA Eggman) is yet again up to his no good tricks. Factories and pollution are spreading like wildfire as he's once again trying to take over the world. Fortunately, the Sonic Heroes are never at rest, and once again wage their battle to defeat Eggman's evil forces.
However, the heroes have landed in double jeopardy. Eggman's madman descendant, Eggman Nega, has escaped from the Ifrit's dimension, and is wreaking his usual havoc in an effort to destroy the world. He's even captured Eggman's top three lieutenants, the ruthless Team Metallix, and reprogrammed them to do his even more evil bidding.
Unlike previous instances of Nega's destruction, Eggman is not fazed. He figures that once he's in control of the world, he can take care of Eggman Nega as he pleases. Unfortunately for Eggman, Sonic the Hedgehog isn't having that. Before he can decide who to dispatch where, he receives a call through the communicator Tails gave him. The message: someone's already on the case. Not just someone, but someones!
Apparently, Sonic's very own sister, Sonia the Hedgehog has already caught wind of Nega's evil and is out to stop him. Sonic is a bit eased, knowing full well of his sister's strength and agility. She also lets him know that she has found and teamed up with a mysterious young hedgehog who can move things with his mind. Sonic instantly recognizes that Sonia is with his newest ally: Silver the Hedgehog. Silver has once again traveled through time to ensure that the future is free of Nega's tampering (though he really ought to just stay here in the present, you know). Knowing that the two hedgehogs are more than capable of handling the situation, Sonic leaves it to them, and resumes dealing with Eggman.
Eggman Nega is well aware that Sonic is busy with his dimwitted ancestor. However, he'd do best not to overlook a certain factor. The S Factor, Sonia and Silver! It's up to you to lead the unlikely tag team of the physically powerful Sonia, and the psychokinetic Silver on their quest to right the wrongs of the evil Eggman Nega!