Tails' latest plane is missing, but this one's got a tracking device - leading Sonic and Tales on a frantic flight to the Mystic Ruins. When they get there, they not only find both Robotnik and Knuckles, but a threat they hoped they'd never have to face again. Back in the city, all seems tranquil for the Mayor and Sally, but you know that can't last - and before you know it, Sonic, Tails and Knuckles are back to try to restore order. What is the mystery that threatens their very existence? Will a cocky hedgehog, a headstrong echidna and an eager fox be enough to save civilization?
Knuckles exploring the Mystic Ruins finds an unconscious Dr. Robotnik. Unknowingly to Knuckles, Chaos is still alive and about to attack him. In Station Square, Sonic tells Sally, Tails, Antoine, Bunnie, Amy and Nate Morgan about his battle with Chaos with Knuckles. Losing Tails' plane, Nate Morgan gives Sonic a device to locate the plane. Sonic and Tails arrive in the Mystic Ruins and find Knuckles and Big, with Froggy unconscious. Sonic and Tails wake up Knuckles and Big, Dr. Robotnik has already awoken and flies away in his machine. Sonic, Tails, Knuckles and Big find the plane, but a water tornado appears and grabs the Super Emerald from the plane.
Back in Station Square, the mayor thanks the Freedom Fighters for recovering the six Super Emeralds, but Chaos appears in liquid form, enters the and absorbs the Super Emeralds. Having seven of the Super Emeralds, Chaos transforms into Perfect Chaos and rampages through Station Square. Antoine, Bunnie, Amy and Nate Morgan help rescue some of the Overlanders while Sally is worrying about Sonic. Sonic, Tails, Knuckles and Big arrive back to find Perfect Chaos. Dr. Robotnik wanting revenge sends out his Egg Carrier to attack Perfect Chaos, but Perfect Chaos destroys the Egg Carrier with one blast.
The spirit of Tikal transforms into her echidna form and tells Sonic and Knuckles that Chaos has absorbed the negative side of the emeralds and is connected to the city's power. Tikal plans to trap Perfect Chaos inside the Master Emerald, however Sonic objects. Tails mentions that Sonic can use the positive side of the emeralds to defeat Chaos. Tikal uses a forgotten echidna ritual to retrieve the emeralds from Chaos and gives them to Sonic. Sonic transforms into Super Sonic and prepares to fight Perfect Chaos to save Station Square.
Sonic calls J. F. Gabrie and finds out that he moved to San Francisco to work with SEGA there. Gabrie assures Sonic that he will still be editing the comics and asks the latter if he has any questions. Sonic runs all the way over to San Francisco and asks very loudly how late Fisherman's Wharf is open for. Gabrie yells at Sonic as he has told him not to do that before, while two SEGA co-workers listen on and label Gabrie as "weird".