Swords of Sanghelios

The Covenant Separatists are a breakaway faction of the Covenant, led by the Elites and "officially" formed after they learned the truth about the Halos at the end of Halo 2.

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, but 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 supporters.

It is speculated that this disgruntled faction is lead by the Arbiter, SpecOps Commander Rtas 'Vadum and Imperial Admiral Xytan 'Jar Wattinr. Fronts of this war include holy city of High Charity, Installation 05, Earth, and areas of space where Covenant ships operate.

How the faction comes to life
The High Prophet of Regret led a botched mission to Earth and was forced into The First Battle of Earth upon discovering what turns out to be the Human homeworld. He escapes to Delta Halo, but is killed by the Master Chief, which is considered a significant failure in the Elites' oath to protect the Prophets.

The remaining Prophets, 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 grown accustomed to their comfortable position in the caste system, and they threaten to resign from the High Council.

Truth then gives command of the Covenant fleets (the Elites' job) to the Brutes. Once there are enough Brutes in place, he secretly orders the Brutes to instigate a brutal genocide of the Elites, so they might 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). The Elites respond, with the help of the Hunters and the Grunts, and war breaks out in High Charity. Later, the 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.

The separatist forces at Joyous Exultation may have had turned the tide of the war in their favor had it not been for Sublime Transcendence's destruction by a UNSC NOVA bomb. You could also say therefore that the UNSC inadvertently blew one of their only chances at winning the war by accidentally destroying their allies.

Military Forces
The Separatists are speculated to be commanded by Rtas 'Vadum and/or the current Arbiter. Their military includes Elite, Grunt and Hunter castes, along with ships of various classes loyal to their cause.

Also involved in this faction is the UNSC Defense Force, which helped the Arbiter on Installation 05 with the killing of Brute Chieftain Tartarus. It is known that alliance has helped each other in the Second Battle of Earth.

It is currently unknown how this alliance will progress in the future, but it is expected by many to become official as the Elites have long respected a number of human traits which would otherwise draw a race into the Covenant, such as in Ghosts of Onyx, when Voro Nar 'Mantakree actually has a look of respect for Kurt.

Units

 * Fleet of Retribution

Trivia

 * 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.