The history of the Covenant differs in this time-line because they set out to the other side of the Milky Way Galaxy before they had a chance to wipe out the other alien species that are in the original Star Trek Universe on a quest to obtain Relics. Once in the Delta Quadrant they built up a new civilization before searching for relics.
At some point in the Delta Quadrant, the Sangheili (Elites) were betrayed by the San 'Shyuum (Prophets) and the other species of the Covenant. After years of fighting, the Sangheili emerged victorious.
After the war, the reformed Sangheili Covenant was split into several orders:
- Prophets- the three highest members of the Covenant High Council, named after the leaders of the earlier Covenant.
- Councilors- the representatives of each of the Covenant controlled planets in the Delta Quadrant.
- Elite- the highest ranking soldiers, pilots, and crewmen of the Covenant, named after the victors of the Schism.
- Brutes- the most aggressive Sangheili warriors, named after the now extinct species. Members of this order would have been made Arbiters in the old Covenant.
- Hunters- heavy weapons specialists, work in pairs, named after the wormlike members of the first Covenant.
- Jackals- the snipers and guards of the Covenant, named after the presumably extinct members of the old empire.
- Drones- rangers who are sent in large numbers and have "jetpacks," named after the flying incectoid species.
- Grunts- the lowest ranks in the Covenant military, named after the Covenant species.
The Covenant fought back and resealed Species 10030 after accidently releasing it. The Borg unsealed them but after discovering that they could not assimilate it, tried to containt it but failed, resulting in a massive war that was ended at the Battle of the Border.