Swords of Sanghelios

"There was honor in our Covenant once, and there shall be again!"

- Thel 'Vadam

The Covenant separatists are a breakaway faction of the Covenant, led by the Sangheili. It was officially formed after they learned the truth about the Halo Installations near the end of the Battle of Installation 05 in November 2552. The separatists no longer look to the Prophets for leadership, and thus have no defined leadership save for the surviving Councilors, although Arbiter Thel 'Vadam and a few other head Sangheili, such as Rtas 'Vadum and Xytan 'Jar Wattinree hold positions of power within their ranks.

Background
The Covenant separatists are made up of the Sangheili, along with some Unggoy and Mgalekgolo loyal to them. The members of the faction were somewhat "united" at the beginning of the Great Schism, although the faction was "officially" formed when they learned the truth of the Halos and since both times, have been fighting the forces loyal to the Covenant, led by the San 'Shyuum with Jiralhanae, Yanme'e, Kig-yar and some Unggoy and Mgalekgolo loyalists.

This disgruntled faction is led by the Arbiter Thel 'Vadam and Ship Master Rtas 'Vadum, since the highest-ranking Sangheili military leader, Imperial Admiral Xytan 'Jar Wattinree was killed by a NOVA bomb soon after announcing the separation of the Sangheili from the Covenant. It is possible the remaining Councilors command the faction from Sanghelios as aides to the Arbiter, offering their counsel to him as they once did with the Prophets. Fronts of this war include the Covenant holy city of High Charity, Installation 05, Earth, the Ark, and areas of space where Covenant ships operate.

Origins of the faction
The High Prophet of Regret led a badly planned mission to Earth, against the wishes of Truth, and was subsequently forced into the Battle of Earth, as he did not know that the planet was the human homeworld. He escaped to Delta Halo, where he was killed by the John-117. Regret's death was used as a justification by the remaining Prophets to replace the Sangheili with Jiralhanae as their protectors. However, this move resulted in great turmoil within the Covenant, with the Sangheili threatening to resign from the High Council.

The High Prophet of Truth then gave command of the Covenant fleets, the post previously held by the Sangheili, to the Jiralhanae. Once there were enough of them in place, Truth secretly ordered them to commit a vicious genocide of the Elites (disguised as a retaliation to an Elite revolt against the other Covenant factions) so they may replace them in society. The Elites responded, with the help of factions of Hunters and Grunts, and war broke out in High Charity with Brute and Elite fleets fighting each other in space around it. Later, most of the Elite Councilors were assassinated by the Brutes at the behest of the Prophets.

Sangheili-human alliance
The shaky-to-steady alliance between the separatists and their former foes, the humans, was forged entirely out of necessity. The UNSC forces were on the defensive, and they had two common enemies that wished for their extinction: the Covenant and the Flood. The alliance of circumstance was forged in the control room of Delta Halo, when Johnson and the Arbiter were coerced to unite in order to prevent Tartarus activating Installation 05. However, the Arbiter persuaded the rest of the Sangheili to join humanity. While the two factions experience some friction, they learn to work with one another for their mutual survival. During the events of Halo 3, the Elites fight alongside humans in battle and save them from destruction.

The devastated UNSC fleet defending Earth were glad to accept the help of the superior separatist warships. The Sangheili' understanding of enemy equipment and Covenant's combat tactics proved invaluable in the Battle of Installation 00. Recurrently the heroes of the battle, Thel 'Vadam and Master Chief, fought alongside one another many times in the desperate and long conflict.

With Truth dead, High Charity destroyed, and Installation 00 essentially lost to the reborn Installation 04 firing, what remained of the Covenant was all but destroyed, with its member species divided into multiple factions. The Arbiter's presence at memorial services for the Master Chief indicated that in the wake of victory, separatist and human forces remained friendly to one another, as they both had made tremendous sacrifices in order to stop Truth and the Covenant forces.

According to the Bestiarum in Halo 3's Limited Edition, the Unggoy were too indecisive to continue the rebellion and the true political motivation of the Mgalekgolo, if any, remains a mystery, although Hunter pairs could have followed the elites they protect. Ship Master Rtas 'Vadum stated that Truth's fleet was destroyed at Installation 00. Had any of the Covenant survived on the Ark or in the ruins of their Fleet, they were either taken by the Flood or killed when the unfinished Installation 04 fired and destroyed itself and heavily damaged the Ark. At the end cutscene of Halo 3, victorious Sangheili depart for their homeworld to ensure its safety.

Over the next six years, the Sangheili continued to wage war against the remaining Prophets and the Brutes. At first, the Elites were at a major disadvantage, as millennia of depending on the Prophets for technology meant that the Elites were unable to properly repair or replace the ships they lost in battle. The odds began to even out when the Prophets "vanished" and the Brutes began to fall back into internecine conflicts.

Commanders

 * Thel 'Vadam (Arbiter)
 * Rtas 'Vadum
 * Xytan 'Jar Wattinree (Deceased at Joyous Exultation when the UNSC's NOVA bomb went off, before the human alliance)
 * Voro Nar 'Mantakree (Deceased)
 * Unidentified Sangheili Shipmaster

Military

 * Sangheili
 * Unggoy
 * Mgalekgolo
 * Huragok
 * UNSC (Allied)

Other notable members

 * Usze ‘Taham
 * N'tho 'Sraom

Units
Fleet units
 * Fleet of Retribution
 * Shadow of Intent
 * Pious Inquisitor
 * Combined Fleet of Righteous Purpose
 * Sublime Transcendence (destroyed by a NOVA bomb on Joyous Exultation)

Ground forces
 * Legions attached to Separatist Navy
 * Special Warfare Group
 * Covenant Special Operations

Trivia
Though the Covenant separatists were called "Heretics" by the High Prophet of Truth, they should not be confused with the heretic faction led by the Sangheili Sesa 'Refumee and destroyed by Arbiter Thel 'Vadamee, although they do have the same goal and beliefs. If remnants of the heretics were still around during the time of Halo 3, they and the separatists would be on the same side, since the heretics also knew the truth about the Halo Array.