Learning of a secret weapon from the diary of his deceased grandfather, Professor Gerald Robotnik, Eggman infiltrates a high-security G.U.N. facility and revives it using a Chaos Emerald. The weapon – a black hedgehog and self-proclaimed "Ultimate Life Form" named Shadow – offers to help Eggman conquer the world, telling him to rendezvous at an abandoned space colony, ARK, with more Chaos Emeralds. Shadow goes to Central City, encountering G.U.N.'s forces after stealing an Emerald. Shadow has vowed to fulfill a promise to a girl, Maria, which he interprets as one of revenge. Shadow blasts through the military force and meets Sonic. After a brief confrontation, Shadow escapes and G.U.N. captures Sonic, whom they mistake for Shadow.

Meanwhile, Knuckles encounters Rouge and Eggman, who try to steal the Master Emerald. He stops them by shattering the Emerald and searches for the scattered shards. Rouge, spying for the government, heads to Eggman's base and the ARK. There, Shadow shows Eggman the Eclipse Cannon, another superweapon created by Gerald, and discloses his plan: to charge the cannon with Chaos Emeralds and use it to take over the world. Rouge appears, offering them a Chaos Emerald to gain their trust.