The Soul Crystal resembles several Raw Emeralds fused together. Somehow, the power of this gem keeps the spirits of the Kohenyu alive and is able to reanimate Kohenyu skeletons. A side effect is the creation of the Spirit of the Herd, an aggregate of all the Kohenyu spirits.
When the Kohenyu were killed by ancient echidnas, their soul somehow became trapped in the Soul 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 crystal. However, he relented when he realized 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.