Sonic ist unter schärfster Bewachung auf Prison Island eingesperrt worden. Seine Freunde beschließen, ihn herauszuholen. Dr. Eggman will in der Zwischenzeit mit Shadow und Rouge die Emeralds von der Insel holen und die Insel danach zerstören.
Under a new alliance, Shadow, Rouge, and Eggman carry out their latest plan. As Eggman launches an attack on Prison Island, Rouge breaks in to steal three Chaos Emeralds, and Shadow sneaks in to plant a bomb which will destroy the island.
As Chris and Tanaka use a small boat to get to Prison Island, Tails and Amy arrive at the island in the X Tornado to rescue Sonic. When Amy accidently runs into Shadow, Eggman comes in to finish her off but Tails jumps in and fights with Eggman. Amy goes in and frees Sonic, who then finds Shadow. The two hedgehogs battle it out.
However, problems arise. Rouge gets trapped in the compound, and Shadow, having another flashback of Maria, breaks away from the battle to go save her. When he gets there, Chris is there too, and pleads with Shadow because Sonic wound up taking the blame for his actions. With less than 10 seconds left before the bomb explodes, Shadow activates Chaos Control, enveloping Rouge and Chris in its energy. The bomb explodes, destroyi
Sonic si costituisce e viene rinchiuso a Prison Island. Eggman arriva con un piano tutto suo mentre Chris, Amy e Tails vogliono far evadere Sonic.
De Sonic se encuentra detenido en una prisión de máxima seguridad en la prisión de la isla, gracias a Shadow y Eggman.
