Swords of Sanghelios

The Covenant Separatists are a breakaway faction of the Covenant, led by the Sangheili and "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 group is lead by the commander in chief the Arbiter and a few other head Elites, including Rtas 'Vadum.

Background
The Covenant Separatists are made up of the Elite, Grunt and Hunter castes within the Covenant's hierarchical society. The members of the faction were somewhat "united" at the beginning of the Civil War of the Covenant, although the faction was "officially" formed when they learned the truth of the Halos and since both times, have been fighting the Covenant Loyalists, led by the Prophets and their Brutes, Drones, Jackals and some Grunt and Hunter supporters. It is speculated that this disgruntled faction is led by the Arbiter, Ship Master Rtas 'Vadum and Imperial Admiral Xytan 'Jar Wattinree. It is possible the remaining Councilors command the faction from Sanghelios as aides to the Arbiter offering their council to him as they once did with the Prophets. Fronts of this war include the Covenant holy city of High Charity, Installation 05, Earth and areas of space where Covenant ships operate.

Origins of the Faction
The High Prophet of Regret led a botched mission to Earth and was forced into The First Battle of Earth upon discovering what turned out to be the Human homeworld. He escapes to Delta Halo, but is killed by the Master Chief, which is a significant failure on the Elites' part to uphold their oath to protect the Prophets.

The remaining Hierarchs, led by the High Prophet of Truth, used this opportunity to replace the Elites with the Brutes as their protectors. However, this move effectively shames and angers the Elites, who have held the position since the founding of the Covenant and they threaten to resign from the High Council.

Truth then gives command of the Covenant fleets, the post previously held by the Elites, to the Brutes. Once there are enough Brutes in place, he secretly orders the Brutes to instigate a vicious genocide of the Elites, so they may replace them in society, disguised as a Brute insurrection against the Covenant and as an Elite revolt to the other Covenant factions, excluding the Brutes and the Prophets, whom were pulling the strings. The Elites respond, with the help of the Hunters and the Grunts and war breaks out in High Charity. Later, the Elite Councilors are assassinated by the Brutes at the behest of the Prophets. When the Elites learn the truth about the Halos, it changes the war significantly and adds the humans to the struggle. Instead of a Great Journey, the Gravemind's revelation regarding the superweapon contradicts the Covenant's belief system and is motivating at least the Arbiter in his eventual opposition to the Covenant as they try to activate Delta Halo later in the game.

Ironically, the Separatist forces at Joyous Exultation may have helped turn the tide of the war in the UNSC's favor had it not been for Sublime Transcendence's destruction by a NOVA bomb. However, at that early point in the Great Schism, both sides of the Covenant still opposed the UNSC. As interstellar communication is not instantaneous, it would have taken some time for an alliance to be forged and for all the elements of the Faction to be informed.

Weapons

 * Type-26 ASG - "Shade"
 * Type-25 Directed Energy Pistol - "Plasma Pistol"
 * Type-25 Directed Energy Rifle - "Plasma Rifle"
 * Type-33 Guided Munitions Launcher - "Needler"
 * Type-1 Energy Weapon/Sword - "Energy Sword"
 * Type-51 Carbine - "Covenant Carbine"
 * Type-50 Sniper Rifle System -"Particle Beam Rifle"
 * Type-33 Light Anti-Armor Weapon - "Fuel Rod Cannon"
 * Type-52 Directed Energy Support Weapon-"Plasma Cannon"

Equipment

 * Deployable Cover
 * Overshield
 * Active Camouflage
 * Flashlight
 * Type-1 Antipersonnel Grenade - "Plasma Grenade"

Vehicles

 * Spectre
 * Type-32 Rapid Assault Vehicle - "Ghost"
 * Type-26 Ground Support Aircraft - "Banshee"
 * Type-52 Troop Carrier - "Phantom"
 * Type-47 Ultra Heavy Assault Platform - "Scarab"
 * Type-25 Wraith - "Wraith"

Commanders

 * The Arbiter
 * Rtas 'Vadum
 * Xytan 'Jar Wattinree (status unknown)
 * Voro Nar 'Mantakree (deceased)
 * Lord Terrence Hood
 * Miranda Keyes (deceased)
 * John 117 (M.I.A.)
 * Avery Junior Johnson (deceased)

Military

 * Elites (All)
 * Grunts (Most)
 * Hunters (Most)
 * UNSC (All)

Units

 * Fleet of Retribution
 * Sangheilian Fleet
 * Special Warfare Group
 * Covenant Separatist Navy

Other

 * Engineers (Unknown) (most likely)

Trivia

 * Though the Covenant Separatists were called "Heretics" by the High Prophet of Truth, they should never be confused or confounded with the factual Heretics led by Sesa 'Refumee.
 * This is not necessarily the first internal dispute in the Covenant's society; when the current Arbiter was assigned to his office, he was reminded by the High Prophet of Mercy that an Arbiter was necessary during the Grunt Rebellion, which was a conflict between the Covenant and its lowest caste, the Grunts.
 * Both the Grunts and Hunters are confirmed allies of the Elites. However, none are seen as anything but enemies in Halo 3. This may be Bungie's decision to not confuse the player of who is enemy and who is ally and there may have been Grunts and Hunters who fought with the Elites and Humans during the last battles of the Great Schism.
 * The Hunters and Grunts may be on another planet in Halo 3, or allowed to resign their duties, explaining their absences.
 * It is a theory that during Halo 3 the Hunters and the Grunts that sided with the Elites were sent back to their homeworlds as there might be conflicts happening there.
 * Another possible reason why there are so few Hunters and Grunts, is that there are only 2 times when Separatists other than the Arbiter are found in-game at all. The first is the Elite special operations team in Floodgate and as they are inserted via Orbital Insertion Pod, there are no Grunts or Hunters present. The second is the attack force in The Covenant, where the Elites are found mid-battle and it's possible that any Grunts or Hunters may have already been killed and thus mistaken for fallen Covenant forces, though no Hunters or Grunts are found in that area, dead or alive. They may also have been killed in the assault on the middle tower.
 * The Separatist Phantoms are green in color, quite unlike the Loyalist Phantoms, which is now a darker bluish-violet color. However, this does not mean all Separatist vehicles' colors are about the same color as well. During the ending cutscene of Floodgate, in the beginning cutscene of the part where the a Separatist Phantom and a couple of Warthogs are seen stopping in the Hangar of the Shadow of Intent, two Banshees of the same colors as Loyalist ones are seen farther away from the hangar. Also in the cutscene, where Marines are sitting around in the hangar with some Elites, a Major Elite can be seen sitting on top of a normal-colored purple Ghost.
 * Probably the most likely explanation for the lack of Separatist Hunters and Grunts, as well as the other Elite ranks such as Honor Guards, Councilors, and Stealth is the fact that there are few allied Covenant in Halo 3 to begin with. Additionally, the Grunts and Hunters were probably taken out in order to prevent confusion to the player. As for the elite ranks, only those seen in game were probably the only amount that the Separatists needed.
 * It is most likely that the Separatists formed a "new" Covenant, given the fact that the groups are now united and probably working on a more balanced caste system, unlike that of Halo: Combat Evolved and Halo 2. Additionally, considering the similarities between the Covenant and the Books of the Bible, a new covenant was established after the sacrifice the races made, similar to Jesus's sacrifice to make a covenant with his people. The new covenant will now very likely work together with the UNSC. This alliance will be supported especially in light of the fact that Elites seem to be aware of the humans' role as Reclaimers.
 * In a lot of the gameplay the Separatist Phantom can be seen just appearing and disappearing from distant sight, this is active camouflage.
 * The Arbiter was able to have all the other Elites separate from the Covenant, thus becoming the Covenant Separatists.
 * Only one individual Zealot has been seen in the Covenant Separatist Force in the Halo 2 Level Uprising, it's unknown that there were anymore Zealots, probably in the background commanding from their imperial posts and keeping safe from the Brute onslaught that murdered many of their superior Councillors.