The Covenant was a religious hegemony based on the worship of the Forerunner race and the artifacts they left behind following the Great Purification. It consisted of no less than eight distinct species from different regions of the Milky Way galaxy structured into a fairly rigid tier system that favored its earliest members as well as the stronger species. The weaker or less intelligent species such as the Unggoy were still ardent believers in the Covenant religion, but were generally assigned to menial labor or, such as on the battlefield, cannon fodder. Because of this structuring there was always tension between the different member species, with major conflicts arising within the Covenant at least two times, once in 2462 during the Unggoy Rebellion, and the second in 2552 during the Great Schism that ultimately destroyed the Covenant.
The Covenant was formed in 852 BCE at the close of the War of Beginnings between the San’Shyuum Reformists and the Sangheili. When the Reformists left their homeworld of Janjur Qom in 2100 BCE, thereby ending the War of Wills, they took with them not just the Forerunner Keyship Anodyne Spirit, but also the belief that the Forerunners should not just be worshiped, but their leftover technology should be studied and used to their advantage. This ideology clashed with the beliefs held by the San’Shyuum Stoics who remained on Janjur Qom, and also the Sangheili who thought the Forerunner artifacts should be studied but not exploited. That conflict in beliefs led to over eighty years of fighting that eventually ended in the signing of the Writ of Union and the formation of an alliance known as the Covenant, whereby the San’Shyuum would occupy most, if not all, of the political positions within the organization, and the Sangheili would be in charge of the military both in space and on the ground.
For the next three thousand years the Covenant slowly grew, absorbing more and more species into their religious alliance and exploring any and all Forerunner artifacts they could find. This process continued in fits and starts until the discovery of humanity, who, because of their designation as Reclaimers of the Mantle of Responsibility by the Forerunners, were classified as such by Oracles the Covenant used to study Forerunner technology. Fearing the members of the Covenant would realize that the Forerunners they worship had elevated another species above the San’Shyuum and collapse their fragile alliance, they labeled all of humanity as heretics and ordered their destruction. This kicked off the Human-Covenant War which would bring nearly thirty years of non-stop fighting and the death of billions of humans.
By 2552 the Covenant had managed to push into the Inner Colonies of human-occupied space, and in August of that year attacked and destroyed the largest colony world, Reach. Only two months later they would discover the location of humanity’s homeworld Earth, and immediately began laying siege to their last military stronghold. At just about the same time, however, one of the San’Shyuum Hierarchs, the Prophet of Truth, began a consolidation of power away from the Sangheili military commanders and to the Jiralhanae who were more loyal to the Prophets. This major disruption in the Covenant power structure, known as the Great Schism, coupled with the loss of the Covenant’s holy city of High Charity to the Flood at just about the same time, crippled the Covenant severely, and led to its collapse, ending the war with humanity.