The origin of the Soul Crystal is unclear. It resembles several raw Chaos Emeralds joined together and fused with power. When the Kohenyu were killed by ancient echidnas, their soul somehow became trapped in the crystal.
Thousands of years later, Knuckles the Echidna visited the Kohenyu Graveyard to dig up a new Master Emerald. The Spirit of the Herd taunted Knuckles for his ancestor's actions and tried to kill him. Knuckles evaded death and discovered the Soul Crystal deep in the mines. After hesitating once and being forced to fight more Kohenyu skeletons, Knuckles prepared to smash the crysyal. However, he relented when he realised that doing so would wipe out all traces of the Kohenyu. Knowing what it is like to lose your people, Knuckles spared the Kohenyu, in return allowing safe passage from the graveyard.