After the set-up scenes, run up through the Mystic Ruin cave and over the bridge to the re-non-floating, Floating Island. Go round to see Knuckles and Robotnik lying prone on the ground and the echidna will tell you that Chaos has returned and taken all the Emeralds.
Tikal's spirit appears and transports Sonic back to the scene of the Master Emerald aflame. Run to the temple and you will see Tikal trying to stop the tribal chief and some warriors from getting to the master Emerald. They barge past and their bad manners are punished as Chaos appears and wastes them all. Run up to Tikal and follow her as she goes toward the Emerald. Once there, you are returned to Mystic Ruin.
You're then woken up by Tails who mentions the Chaos Emerald that is left in his plane. Take the minecart to the rainforest and drop down through the canopy. A flow of water appears and carries the Emerald away from the plane's nose. Chaos now has all seven Emeralds.
A cut-scene shows Chaos laying waste to Station Square and turning into Perfect Chaos. He then blows Eggman away with one dismissive blast. Tikal appears and tells Sonic he must stop Chaos and trap him inside the Master Emerald, she then conjures the seven Emeralds away from the monster. Sonic's five fellow adventurers show up and Tails tells the hedgehog he should use the Emeralds to become Super Sonic and finish Chaos off once and for all.
You begin with 50 rings and as long as you don't drop below 50 you'll remain as Super Sonic. Fortunately, there are loads of rings to be found on the ramps to keep your total topped up, but you still have to be quick as you will lose one ring every second. Because the fight is on water if you do revert back you will die because only Super Sonic has the pace to travel on water.
You also need to be quick in order to hurt Chaos as you have to zoom up through his body and burst out of his head. If you're not going fast enough you will flop down without reaching his brain. There are travelators on the ramps which will give you a speed boost and be sure to avoid Chaos' water attacks that slow you down.
Hit him three times and Perfect Chaos will return wiith even more power and firebolts to shoot at you. Hit him three more times in this incarnation and the battle is won.
This final battle may sound tough but it's actually not too difficult. Just keep using the ramps to collect the rings and zoom off the travelators, head straight for Chaos while dodging his attacks and burst through him six times in total. The biggest worry is losing all your rings and transforming back to Sonic, but if you're quick enough this shouldn't be a problem
With Perfect Chaos destroyed he reverts back to his initial, puny form. As Sonic and his pals look on Tikal and a group of chao circle Chaos and take him away. Sonic notices Eggman skulking away. As Tails turns to speak to his pal he sees Sonic running off into the horizon.