Standing as vastly more different than any of Chaos' previous forms, Perfect Chaos is a several-stories-tall monster composed entirely of water. Its head resembles a snake with razor-sharp teeth and a large mouth that extends far beyond its eyes, which are green and have slit-like pupils. It also has flaps of skin hanging from just behind its eyes and a fin on top of its head.
4,000 years ago, Chief Pachacamac of the Knuckles Clan and his men attacked the shrine in the Mystic Ruins, home to Chaos and its family of Chao that it protected, to seize the Chaos Emeralds and Master Emerald there for war, injuring both the Chao and their friend Tikal. In a fit of anger and sadness, Chaos became Perfect Chaos with the Chaos Emeralds' negative energies, killing nearly the whole Knuckles Clan, Pachacamac and his men included, and laid waste to their entire civilization. However, Perfect Chaos would not stop its rampage and would have destroyed the rest of the world too had it not been for Tikal, who sealed herself and Perfect Chaos inside the Master Emerald.
Four millennia later, Chaos was freed by Dr. Eggman, who sought to transform it into Perfect Chaos and use it to destroy Station Square. Still brimming with rage, Chaos remained under Eggman's command while the doctor collected the Chaos Emeralds for it so it could continue its rampage. When Eggman failed, Chaos rebelled against Eggman and got the Emeralds itself, becoming Perfect Chaos again and attacked Station Square, during which it destroyed the second Egg Carrier. When Perfect Chaos released the seemingly-drained Chaos Emeralds however, Sonic the Hedgehog used them to become Super Sonic and defeat Perfect Chaos. With its defeat, Perfect Chaos reverted back to normal and its anger was neutralized by Super Sonic's power, returning it to the peaceful creature it once was.
When Dr. Eggman used the Time Eater in an attempt to alter Sonic's past, Sonic faced and defeated Perfect Chaos again, this time in his normal form.