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 its commander in chief the Arbiter and a few other head Elites, including Rtas 'Vadum and Xytan 'Jar Wattinree.

Background
The Covenant Separatists are made up of the Elite, Grunt and Hunter castes (Grunts and Hunters are only seen in Halo 2 as allies.) 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 badly planned mission to Earth and was forced into The First Battle of Earth upon discovering that the planet was the Human homeworld. He escapes to Delta Halo, but is killed by the Master Chief. Regret's death was used as a justification by the remaining Prophets to replace the Elites with the Brutes as their protectors. However, this move resulted in great turmoil within the Covenant, with the Elites threatening 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 were enough Brutes in place, Truth secretly orders the Brutes to instigate 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 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. Either way, the UNSC had no choice, since they sent a strike force to eliminate the humans at Onyx and get the forerunner artifacts, still in the belief of the religion that brought the Schism on them. Though the humans were trying to harvest the technology of the planet,while the elites were trying to preserve it.

Weapons

 * Type-25 Directed Energy Rifle - "Plasma Rifle"
 * 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 Gun"
 * Type-52 Directed Energy Support Weapon - "Plasma Cannon"

Equipment

 * 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 Assault Gun Carriage - "Wraith"
 * Seraph-class Starfighter
 * CCS-class Battlecruiser
 * Assault Carrier

Commanders

 * The Arbiter
 * Rtas 'Vadum
 * Xytan 'Jar Wattinree (status unknown)
 * Voro Nar 'Mantakree (deceased)
 * Lord Terrence Hood
 * Miranda Keyes (deceased)
 * John 117 (MIA)
 * Avery Junior Johnson (deceased)
 * N’tho ‘Sraom
 * Usze ‘Taham

Military

 * Elites (All)
 * Grunts (Most, likely all after the war. During the war about the half of all.(Not seen in-game due risk of confusing enemy with friend. A few Separatist Grunts took part in the Battle of Installation 00, but they cannot be interacted with by the player and are seen at a distance. )
 * Hunters (Most, likely all after the war. During the war about the half of all.(Not seen in-game due risk of confusing enemy with friend.)
 * UNSC (All)
 * Possibly the Jackals and Drones after the war is over. (The Elites have been known to welcome the enemies remaining allies into their military)

Units
Covenant Separatist Navy:
 * Fleet of Retribution

Covenant Separatist Army:
 * Legions attached to Separatist Navy
 * Special Warfare Group
 * Covenant Special Operations

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 the Reclaimers. This "New Covenant may even include humanity as a member species, because both the rebels and UNSC have thrown their lots in together.
 * In a lot of the gameplay the Separatist Phantom can be seen just appearing and disappearing from distant sight, this is active camouflage.
 * 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 Councilors.
 * The Separatists are, currently, the most powerful faction in the Halo Universe.
 * The Separatists could have possibly saved the human race from extinction.
 * If the Heretics were still around during the time of Halo 3, the Separatists would be on the same side as the Heretics, since they also knew the truth about the Halos.