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This article contains plot details.
The game begins with Sonic and Tails on the case to find some missing Chao. Eggman Nega, who is once again disguised as Dr. Eggman, has captured the Chao. He plans to feed them to an inter-dimensional beast called "Ifrit", which will cause the beast to become invincible. However, the seven Chaos Emeralds are need to open a portal to Ifrit's world.
Eggman Nega hires Rouge the Bat, who is unaware of who he really is, to find the Chaos Emeralds. However, the Master Emerald has also gone missing and Rouge runs into Knuckles. With no other choice, Rouge and Knuckles team up.
Silver once again returns from the future, it having now been ruined by the Ifrit. In an attempt to fix things, Silver goes to find the remaining Chao and hide them. Along the way, Silver runs into Espio and Espio decides to keep an eye on him.
Metal Sonic is soon sent out by the real Dr. Eggman in order to find out what Eggman Nega's plans are and to find Shadow. By reading Professor Gerald's journal, Eggman Nega found out about Ifrit. Shadow and Metal Sonic then set out to retrieve the Chaos Emeralds before Eggman Nega can.
Near the end, all of the teams meet up. After the portal to Ifrit's world is opened, Eggman Nega sends out Metal Sonic 3.0 to awaken it. Ifrit then possesses the minds of Sonic, Tails, Knuckles, and Rouge. Regardless, the other teams are able to defeat him. Shadow and Metal Sonic close the portal with Eggman Nega, Ifrit, and themselves trapped on the other side.
Metal Sonic begins to tear his chassis apart and pulls out the last Chaos Emerald. using the emerald, Shadow and Metal Sonic teleport home while Eggman Nega is left there. All the Chao are then rescued and the Master Emerald is found. However, Rouge takes the opportunity to steal the Master Emerald and runs off. Silver returns to his future and Espio returns to the Chaotix.
The game received average reviews from critics.