The Covenant Separatists, also known as the Sangheili Rebels, the Heretics, the Traitors, the Human-Sangheili Alliance or the Chosen Ones, but more recently renamed the Swords of Sangeheilios, were a group of Covenant led by the Elites who broke away from the leadership of the Prophets when the truth about the Halo Array was revealed.
The rebellion was led by the Arbiter and Shitmaster after the Prophets betrayed the long-loyal Elites and allowed the Brutes to kill them. At the same time, the truth about the Halo Array was revealed to the Elites by the Humans and they broke away from the Covenant entirely, taking with them a large portion of its fleet, arms and vehicles.
The Elites, Grunts and Hunters in the rebellion later allied themselves with the Humans and utterly smashed the Prophets and their Brute minions, later leading to the Elite-Brute War. Following the war, most if not all of the Brutes were exterminated and the Separatists main problem was re-establishing order amongst the remaining fledgling factions of the Covenant. Most accepted the rule of the Arbiter, but the Storm Covenant defected due to their lingering hatred of Humans.Despite the loyal allies that they once were, it appeared as if the relationship between the Elites and the Humans soon began to break down. After destabilising the Arbiter's rule, the UNSC was kept under close watch by the League in case the fools at ONI decided to start another war. Spartan Locke helped prevent this by saving the Arbiter and helping him destroy the Covenant, but Cortana emerged with a load of Guardians to conquer UNSC space, so the future of their alliance remained unclear.