The Xel'naga modified the protoss for thousands of years before they descended to the surface. The protoss worshipped them as gods and learned much from them. However, as individual psionic and scientific achievements became more important, the protoss tribes began to separate themselves from each other as the protoss psychic bond vanished. The xel'naga now felt they had pushed the evolution of the protoss too quickly and abandoned their first creation.
The protoss tribes, feeling betrayed by their gods, fell into a massive civil war called the Aeon of Strife which lasted countless protoss generations, causing their technology to fall to a Stone Age level. The Strife finally ended when the mystic Khas recreated the bond, calling it the Khala, pacifying the tribes and teaching them some of what he learned from the xel'naga.
The protoss religion centers around the Khala, and it is the center of all their psionic power. In order to maintain its purity, protoss culture, led by the Conclave following the Aeon of Strife, became very conservative, leading to philosophical differences between the Khalai and the Dark Templar—the latter being a group who refused to join the Khala.
The Dark Templar were exiled a thousand years ago, and the Khalai watched over much of the universe, establishing colonies, engaging in wars with some of the alien races and avoiding contact with the lesser species. They did not interfere when the terrans arrived in the Koprulu Sector, virtually in their shadow, until the zerg entered the Sector and began attacking the terrans. In an effort to stem the infestation, the Conclave ordered the executor, Tassadar, to destroy the tainted worlds, starting with Chau Sara.
The protoss suffered heavy losses during the Brood War and are being forced to rebuild their civilization, but are protected from the zerg by a xel'naga temple on Shakuras.