Sonic is relaxing in Mystic Ruin when Tails tells him all is not done yet. They head to the Emerald Shrine where they find Knuckles and Eggman after Chaos has attacked them. Tikal light gives Sonic one last vision of the past. Sonic sees that Chaos is full of rage from what the Echidna Tribe did, and so Tikal sealed him away in the Master Emerald.
Sonic and Tails run to the jungle to get the last emerald from Tails' plane but they are a second too late. Chaos 6 turns to Perfect Chaos, and turns Station Square into a watery hell.
Sonic heads back to Station Square where Tikal light turns into Tikal, and talks to him. Eggman makes a very pathetic attempt to stop Chaos. Perfect Chaos spits out the emeralds, now drained of their negative energy. The entire gang turns up and gives the Emeralds to Sonic, and he turns into Super Sonic. They battle, and Perfect Chaos turns back into Chaos Zero. A bunch of chao surround him, and he becomes gentle. Tikal thanks them and takes Chaos back to the Master Emerald. Sonic dashes off once again.