It is revealed that Chaos has survived. Eggman mutters about his hatred of Sonic, knowing that he cannot spoil his master plan. He stops and spots Chaos, who mauls him. Angel Island has fallen again. Knuckles knows this as well. He decides to take the Chaos Emeralds to Sonic as advice, but spots Eggman lying on the ground. Eggman's mutter of pain is "This is terrible!! C-Chaos is..." Knuckles asks "Is what?", but is interrupted when Chaos appears and attacks them both, stealing the six Chaos Emeralds.
Sonic is relaxing by a tree when Tails tells him that Angel Island has fallen. When they get there, they spot Knuckles and Eggman in serious pain and are exhausted. Knuckles tells Sonic and Tails that Chaos has survived and has stolen his Chaos Emeralds. Eggman heads off on his mobile and goes inside the Egg Carrier 2, a replacement flying fortress, found in the underwater by Omega, Orbot, Cubot, Decoe and Bocoe. Knuckles tells Sonic about Chaos' ferocity and states that if he gets the last Chaos Emerald, death will come. Sonic knows that he'll find it before the renegade does. Tea suggests that they'll lure Chaos into a trap, but Sonic is sent to the past for the last time. This time he spots the Alter under attack from the Knuckles clan, who knocks Tikal to the ground and injures many Chao. This enrages Chaos, who devours the Chaos Emeralds and goes berserk. Sonic heads over to Tikal and asks if she's okay. Tikal realizes Chaos is wreaking havoc and seals him and herself within the Master Emerald for an extremely long period of time.
Sonic returns to the present day. Tails says that they have to get the last emerald before Chaos does. They head over to Big's hut and spot the X-Tornado. Chris gets the Red Chaos Emerald and he, Sonic and Tails are about escape with the emerald. Suddenly, Chaos arrives and attacks Chris. Sonic and Knuckles rescue Chris, but Chaos devours the last Chaos Emerald. As it has all 7 Chaos Emeralds, Chaos turns into Perfect Chaos, and goes on a rampage in Domino City and attacks Station Square, flooding two cities. Sonic realizes how vicious Chaos really is, spots the Egg Carrier 2 from the corner of his left eye and knows that Eggman's after the renegade. Transforming his Egg Carrier 2 into Battle Mode, Eggman attempts to engage in combat, but Chaos sears the fortress to ash with a massive beam of fire. Sonic is getting aggravated with Chaos' ferocity, but Tikal arrives. Tikal the Echidna, who came from the past, arrives to tell everyone about Chaos. Sonic realizes Tikal sealed Chaos in the Master Emerald. She states that her heart's been always with the Master Emerald as well as Chaos', but he's full of rage and tragedy. If this happens, he'll sear New Earth like he did centuries ago. Perfect Chaos sends the Chaos Emeralds flying just 5 seconds before he absorbs their power. Tikal declares that Chaos be sealed in the Master Emerald, but Sonic states that it won't change on how Chaos feels from within, his heart will still remain in turmoil and his anger won't fade. They are faced with only one option: Destroying the anger and rage within Chaos' heart. Sonic's allies gather the Chaos Emeralds and state that Chaos has absorbed their negative power. Closing his eyes and using the positive energy of his friends and the citizens of Station Square, Sonic restores the Chaos Emeralds to their normal states and transforms into Super Sonic, and he flies off to engage the gargantuan dragon in battle.
After the first half of the battle, Perfect Chaos drowns, but re-emerges and starts screaming. He then opens his eyes, spots Super Sonic, and the second half of the battle begins. Three phases later, Chaos is reverted to his normal form, shape and size, and his rage faded. He spots several of his organic kin, the Chao, and knows of their peacefulness. Tikal arrives and tells Chaos that the Chao have been living peacefully with mankind for a long time and continue to do so. With the fighting over and harmony restored, the circle of life moves on. She and Chaos then return to their time. Seconds after, Eggman flies away. Peace is back once more, and Sonic runs off in search of more adventures.
- Perfect Chaos looks more like the Loch Ness monster due to an increased "back" size and several new tentacles. Perfect Chaos also uses a few more powers, like absorbing projectiles like a sponge and then spitting them back at the attacker through its mouth, using its tentacles to attack (he is seen splitting skyscrapers in half with them), and creating crystal spires and an energy shield. He also controls water and, if you look closely before his battle with Super Sonic, his tongue is much longer than his enormous jaws. He can also fire an energy beam, which he uses to burn the Egg Carrier 2 to cinders.
- Perfect Chaos has his original roar which other monsters like the Biolizard also received with a pitch change. Chaos also now seems to have gained a new damage "cry", because when he gets damaged he will scream with a very sad tone in his voice. This new "cry" was actually and combine with explosion sounds effects when Super Sonic delivers the final blow.
- The Egg Carrier 2 in Battle Mode similar to the Egg Carrier's transformed state.
- Solomon Muto said that he will fix Kame Game after Perfect Chaos attacks Domino City. Yugi's grandfather's game shop was heavily damaged by Chaos.
- In The Road to El Dorado, upon both Miguel and Tulio seeing the giant stone Jaguar activated by Tzekel-Kan, they perform a seldom seen double girly scream. In this episode, Joey and Tristan seeing Perfect Chaos revived itself, they perform a seldom seen double girly scream.