One day, Sonic the Hedgehog is approached by Miles "Tails" Prower and Knuckles the Echidna, who give him a message from Dr. Eggman, saying he has developed an ultimate weapon that will take over the world in three days. As Sonic, Tails and Knuckles form a team in order to stop him, other teams are formed elsewhere with their own motives. Amy Rose, who is constantly on the heels of Sonic, teams up with Cream the Rabbit and Big the Cat, who are both searching for their missing friends, Chocola the Chao and Froggy, in order to chase after a clue leading to the whereabouts of all of them. Rouge the Bat, infiltrating one of Eggman's bases in search for a reputed treasure, discovers both a capsule containing Shadow the Hedgehog, who was presumed dead following the events of Sonic Adventure 2, and a robot named E123-Omega who had been abandoned by Eggman. Realising Shadow has lost his memory and Omega has his own vendetta against Eggman, the trio form a team to go after him, hoping to find clues to find out more of Shadow's identity along the way. Finally, the Chaotix Detective Agency, consisting of Vector the Crocodile, Espio the Chameleon and Charmy the Bee, receive a walkie-talkie from an anonymous client wishing to hire their services. Having a policy of never turning down any work that pays, the team take on the mysterious client. As the teams push on their travels, Team Rose discovers Chocola and Froggy have been kidnapped by Eggman, whilst Shadow comes across evidence suggesting that he is in fact an android.

As each team soon arrives at Eggman's Egg Fleet, they each manage to beat Eggman in battle, with Team Rose reuniting with Chocola and Froggy whilst Rouge hears from Omega that the real Shadow may be out there somewhere. Meanwhile, Team Chaotix discover that the Eggman that had been concocting this plan was a fake all along, as the real Eggman, revealed to be the Chaotix's client, had been imprisoned. The true mastermind is soon revealed to be Metal Sonic, who had disguised himself as Eggman in order to copy data from each of the teams, allowing to transform into the powerful Metal Overlord so that he can finally prove himself to be the best Sonic. Thankfully, Sonic manages to use the seven Chaos Emeralds to transform into Super Sonic and, along with Tails and Knuckles, manages to beat Metal Sonic, returning him to his regular form. As Metal Sonic laments his loss, Sonic tells him he's ready for any challenge he throws at him before going off with his friends on another adventure.