Prior to becoming a legendary force of destruction, Chaos was the peaceable guardian of a group of Chao living in the Mystic Ruins. He worked at this task for an unknown period of time, until he eventually met Tikal when the Knuckles Clan settled near his home. The two soon became friends despite Chaos' inability to speak, and for a time all was well. But as the war between the Knuckles Clan and the inhabitants of the Mysterious Cat Country escalated, clan leader Pachamac sought to seize the seven Chaos Emeralds that belonged to Chaos' charges. When he and his warriors attacked, Chaos was corrupted by outrage and destroyed them, going on a rampage that might have spread to the rest of Mobius had Tikal and the Chao not been able to seal him inside the Black Emerald, putting an end to his threat-for a time.
Chaos' legend fell into obscurity, and it was only as Dr. Eggman looked over the file network of his deceased counterpart Dr. Ivo Robotnik that he discovered Chaos' existence and began scheming to claim the creature's power for himself. Using an army of Robians, he excavated the Black Emerald from the midst of the Mysterious Cat Country, cracking it with a hammer blow only to discover that Chaos' imprisonment had weakened him. However, Chaos remained strong enough to lead Eggman to an ancient inscription that revealed to him that Chaos could be restored using the seven Super Emeralds created when the Chao imprisoned him and drained his powers, or by using seven Emeralds equally powerful. When Eggman shattered the Master Emerald into pieces to see his goal fulfilled, a part of Chaos' substance landed in the Mysterious Cat Country and was swallowed by Froggy, the frog companion of Big the Cat.
Eggman was able to help Chaos on his first step towards recovery by using Froggy's now altered DNA to restore some of Chaos' strength. Thus fortified, Chaos infiltrated the Hidden City of the Ancients and soon became involved in a battle with the security forces. He was then challenged by Sonic the Hedgehog, whom he proved too weak to defeat at that point in time. Later, Chaos attacked Sonic, Miles "Tails" Prower, and Knuckles the Echidna, stealing from them Master Emerald shards in order to evolve into his Chaos 2 form. To make matters worse, Eggman arrived with two more recovered shards to boost Chaos to his fourth form, which the trio briefly managed to imprison in an orb of glass. Unfortunately, Chaos 4 broke free and departed with Eggman, leaving the heroes to their own devices.
Returning to Eggman's Egg Carrier, Chaos soon absorbed two more Emeralds and reclaimed its tail from Froggy, regaining much of its strength as it grew into Chaos 6. Knuckles and Sonic valiantly attacked it, only to be caught in a frozen trap and have Chaos try to consume them. Luckily, Knuckles was able to resist long enough for Sonic to help him break free, and the two of them then shattered a flash-frozen Chaos. Despite this, Chaos survived, and after attacking both Eggman and Knuckles, he recovered the last of the Super Emeralds - first from Tails' Tornado biplane and then from Station Square's power planet-in order to become Perfect Chaos, upon which he launched a devastating assault on the Hidden City of the Ancients.
Perfect Chaos flooded the streets of Station Square, forcing the Knothole Freedom Fighters and their ally Nate Morgan to work quickly in order to save many citizens. For all their valiant efforts, they could not deal with the creature themselves, and even Sonic and Knuckles were at a loss. Dr. Eggman returned with a second Egg Carrier, intent on reclaiming Chaos for himself, only for Perfect Chaos to betray him once again and blast his ship out of existence. Tikal then arrived and shared with Sonic a vision of Chaos' past, helping him to understand the threat posed by the creature. Using her powers, Tikal removed the Super Emeralds from Perfect Chaos, delivering them to Sonic so that he could use them to seal Chaos within a restored Master Emerald. Drawing on the untouched positive energy of the Emeralds to combat Chaos' negative power, Sonic transformed into Super Sonic and engaged the massive creature. For all of Super Sonic's power, though, he found himself in a deadlock with Perfect Chaos, unable to weaken him enough to bring him down. While the two titans clashed, Knuckles set about finding a way to short-circuit Perfect Chaos so as to defeat him once and for all. Using his immense strength to lift an entire power plant, Knuckles restored its connections and set electricity flowing just as Super Sonic led Perfect Chaos into the midst of the electric wires. Chaos reverted back to his original state, seemingly also made peaceable again as the Super Emeralds returned to their Chaos forms. Tikal then caught her up her old friend in a magic spell, teleporting them both to another zone from which they have not since emerged.