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 no longer look to the Prophets for leadership, and thus have no defined leadership save for the surviving Councilors, although The Arbiter 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 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 by mistake 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 might 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 believing in the religion that brought the Schism on them. Though the humans were trying to scavenge the Forerunner technology, while the separatists were trying to preserve it from being used.

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"
 * All human weapons from UNSC (although Covenant never use them)

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"
 * Type-52 Anti-Aircraft Artillery - "Anti-Air Wraith"
 * Seraph-class Starfighter
 * CCS-class Battlecruiser
 * Assault Carrier

Commanders

 * Thel 'Vadamee (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, possibly all after the war. (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, possibly all after the war.(Not seen in-game due to risk of confusing enemy with friend.)
 * UNSC (All)
 * Possibly Drones and Jackals after the war. Elites have been known to allow enemies remaining allies into their military. This is not a mercy Brutes would receive due to the hatred between the two species.

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)

Reasons for the Absence of Grunts and Hunters

 * This was internally done by Bungie to avoid any possible confusion between ally and enemy.
 * Reassigned duties for both species, or sent to protect their homeworld and/or Sanghelios due to the absence of the Elites.
 * Not seen by the player, due to the few times Separatists (not counting the Arbiter) are seen. However, this is most likely false, as they would have been seen on the Shadow of Intent at the end of Floodgate, and the other cut scenes it is featured in.
 * Led an Assault on the middle tower in The Covenant, where they died. This is supported by the fact that if you are fast enough with the Hornet you can fly to the middle tower where you can see Elites, Grunts, and Jackals lie dead faced against the door. This is also unlikely because the Hunters would have easily defeated the Brutes, and Miranda Keyes only mentions the Arbiter and the Elites being at the tower.
 * Yet another reason 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.

Trivia

 * Though the Covenant Separatists were called "Heretics" by the High Prophet of Truth, they should not be confused with the factual Heretics led by Sesa 'Refumee and destroyed by the Arbiter. If remnants of 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 Halo Array.
 * 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.
 * 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 Loyalists 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.
 * In a lot of the gameplay the Separatist Phantom can be seen just appearing and disappearing from distant sight, using inbuilt 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 posts and keeping safe from the Brute onslaught, that murdered many of their superior Councilors.