The Chaos Emeralds originated from the Black Comet and were created by the Black Arms thousands of years ago, much like the Babylonian aliens created the Arc of the Cosmos. The Chaos Emeralds ended up on earth more than 4,000 years ago, mutating the wildlife, resulting in “mobians” (mobilizing animals). Both the Black Arms and mobians are able to utilize the Chaos Emeralds and chaos energy.
Since the Emeralds landed in the wilderness instead of human settlements, few humans were mutated. The Robotnik family gained mutations from proximity to the Emeralds on the Ark, explaining Eggman and Maria’s strength (Lost World and The Doom/Lost Impact, respectively). Otherwise, most humans are normal.
Chaos, a mutated chao, also came to be because of the Emeralds. Being in such close proximity to all seven Emeralds and the Master Emerald, he became far more powerful than the average mobian, achieving "yokai" status.
This phenomenon was why Black Doom showed such interest in earth and creating Shadow, a stronger soldier. The Glyphic Canyon, built over 2,000 years ago, was partially built to study mobians and how chaos energy affected the planet.
Professor Gerald learned this and included it in his notes secretly.