Great Schism

The Covenant Civil War, also known by members of the Covenant as the Great Schism, is a war between the two factions that split apart in November 2552.

Cause
After the Prophet of Regret was killed by the Demon, the Prophets, most notably the High Prophet of Truth, deemed it necessary to reorganize Covenant society, replacing the Elites with Brutes as the Prophets' protectors. The Elites viewed this as a violation of the principle the Covenant had been founded upon and threatened to resign from the High Council and arguing that if Truth had not withdrawn the Phantoms that had been on route to Regret's location, the Prophet's death would have been prevented, and the Demon would have been killed.

To further deform the Covenant, Truth then gave command of the Covenant fleets (the Elites job) to the Brutes. Once there were enough Brutes in place, Truth instigated the war by secretly ordering the assassination of all ruling Elites on and around High Charity, and presumably, the entire galaxy and beyond. This is disguised as a Brute insurrection against the Covenant to the Elites, the Hunters, and most Grunts, and as an Elite revolt to the other factions (excluding the Brutes and the Prophets).

Factions
When war broke out on High Charity, the two sides were quickly decided, leaving the Covenant split in two, though one could say that it "truly" split when the Elites learned the truth about the Halos and the Great Journey. One force, the Covenant Loyalists consist primarily of the Prophets, Brutes, Jackals, Drones and, apparently, a number of Grunts and Hunters while the Covenant Separatists seemed to comprised mostly of Elites, with most Hunters and many Grunts also breaking away. The Grunts allegiance was depending on who their commanders at the time were, so many joined the Loyalists, while most Grunts under command of Elites such as the Special Ops joined the Separatists. Furthermore, it appears that an alliance of circumstance galvanized in the control room of Delta Halo has tied the fate of the UNSC with that of the Covenant Separatists.

Sangheili-Human Alliance
Since the events of Halo 2, the Elites have held a mutually beneficial alliance with the UNSC forces During the events of Halo 3, many times do Elites fight alongside Humans, either on foot or in space.

The devastated UNSC Fleet was glad to accept the help of the superior Separatist Warships. The Elite's understanding of enemy equipment and combat tactics proved invaluable in the battle for Installation 00 (The Ark). Frequently the Heroes of the battle, the Arbiter and Spartan 117, fought alongside one another in the desperate and long conflict.

Since the events of Halo 3, the Elite's relationship with Humanity is generally vague and unclear, however the tone of Halo 3's final cutscene implies that it is not a bad one.

2552
September 22: October 20: October 21: October 22: November 3
 * Installation 04 is destroyed by Human forces. Its Monitor, 343 Guilty Spark, escapes to Threshold. The Fleet of Particular Justice is wiped out. The fleet's secondary flagship, the Ascendant Justice, is captured by humans.
 * A Covenant Artifact Retrieval team led by Sesa 'Refumee is investigating the Gas Mine of Threshold when he encounters 343 Guilty Spark. Inspired by Spark's words, 'Refumee rebelled against the High Prophets of the Covenant.
 * The Supreme Commander of the Fleet of Particular Justice is tried before the High Council and sentenced to death.
 * The High Prophet of Truth overrides the council and makes the Supreme Commander an Arbiter of the Covenant. Truth then sends him to kill Sesa 'Refumee and destroy his rebellion, which they dub "Heresy".
 * The First Battle of Earth. The defeated High Prophet of Regret is forced to retreat to Installation 05, pursued by the UNSC In Amber Clad.
 * The Arbiter and a SpecOps Commander, Rtas 'Vadumee leads a team of SpecOps forces to Threshold, where they kill Sesa 'Refumee and successfully crush his rebellion.
 * The Master Chief tracks down and kills the Prophet of Regret on Installation 05.
 * High Charity arrives at Installation 05. Witnessing the assassination of the Prophet of Regret, the Prophet of Truth replaces the Honor Guard Elites with Brutes. Insulted, the Elite Councilors threaten to resign from the High Council.
 * The Arbiter and Tartarus are sent to retrieve The Index. The Arbiter successfully takes the Index, but Tartarus tries to kill him and takes the Index from him, as he was secretly ordered to do so by the Prophet of Truth.
 * Most of the Elite Councilors are taken to the surface of Installation 05 where they are massacred by the Brutes.
 * Tartarus declares war on the Elites, and the Battle of High Charity begins. Fighting between Elite and Brute forces breaks out all over the Holy City. As word spreads, fighting takes place throughout the fleet, as Elite- and Brute-controlled ships attack one another.
 * Flood invade High Charity in the middle of the battle using the UNSC frigate In Amber Clad.
 * Tartarus attempts to activate the Halo.
 * The Arbiter, with the help of Sergeant Johnson and Rtas 'Vadumee, kills Tartarus.
 * The battle in and around High Charity ends with the Flood in control of the city. The Brute and Elite fleets remaining around the city-station continue to destroy each other.
 * The Prophet of Truth takes the Forerunner Ship to Earth, to join The Second Battle of Earth. The Brute forces there are already engaged in fighting with the UNSC. Unbeknownst to the Prophet of Truth, the Master Chief is on the ship, with the intention of "finishing the fight".
 * the UNSC Prowler Dusk witnesses the battle between Elite- and Brute-held ships above Delta Halo, both fighting each other pausing only to stop an immediate outbreak of the Flood from the ringworld, and links up with Battlegroup Stalingrad.
 * Major Domo Voro 'Mantakree kills his Ship Master, Tano 'Inanraree, while he is attempting to allow the Flood to enter the ship, assumes command, and becomes the de facto leader of the Second Fleet of Homogeneous Clarity. He leads his forces to Joyous Exultation, pursued by the Brute Gargantum and his ships.
 * Imperial Admiral Xytan Jar 'Wattinree plans to lure the Brute leadership to Joyous Exultation, and plans an ambush for them. He deploys the newly-promoted Fleet Master Voro 'Mantakree to Onyx to recover the Forerunner technologies there, and prevent the UNSC forces there from claiming it themselves. A NOVA bomb captured by the supercarrier Sublime Transcendence devastates the planet moment after Mantakree's forces leave, the survivors joining Mantakree at Onyx.

In Halo 3, the Grunts and Hunters are never encountered as allies, and were probably deployed by the Seperatists elsewhere. According to the Bestiarum in Halo 3's Limited Edition, the Grunts were too indecisive to continue the rebellion, and the true political motivation of the Hunters is a mystery.

The Covenant all attack Earth in unison, including Hunter and Grunt Loyalists. When the portal to the Ark is opened, all Covenant Loyalist forces leave Earth and enter the void, just as the Flood entered Earth through an infected ship. Shortly after, a flotilla of Elite spacecraft arrive at Earth and proceed to glass half the continent to end the Flood outbreak. The Elite forces then join with the Forward Unto Dawn and Aegis Fate and follow the Loyalist armada to the Ark to prevent the Halos from being fired.

When the Human-Elite force arrives, they are soon engaged by a Loyalist fleet triple their size. According to the Ship Master the Seperatist Fleet destroyed the Loyalist Fleet in this battle while the Forward Unto Dawn was forced to land on the Ark as it couldn't withstand such a massive battle for too long. As the battle in space occurs, Human troops and armor are deployed into the surface to fight the Covenant forces. Human and Elite forces proceed to shut down the shield around the Control Room. Ironically, as soon as the shield meant to block the Flood is shut down, High Charity appears, spewing Flood across the Ark and presumably containing Gravemind. Fighting through Loyalist and Flood alike, the Master Chief and the Arbiter finally confront and kill the Prophet of Truth, preventing the activation of the Halos.

With Truth dead, it is unknown what exactly the remaining Loyalist forces did. They presumably escaped, or perhaps were completely destroyed, since no more Brutes or their allies are seen for the rest of the game. At the end cutscene of Halo 3, we see the victorious Elites departing for their homeworld. It is most likely that the Covenant has been disbanded, and with the war over and the Flood threat effectively ended, each race probably returned home to rebuild. Although, Shipmaster Rtas 'Vadum states that Truth's fleet was destroyed, so, had any of the Covenant survived on the Ark or in the ruins of their fleet, they were either taken by the Flood or definitely killed when the unfinished Installation 04 fires and destroys itself and presumably the Ark.

March 3 2553 The Humans and the Elites make a memorial to commemorate those who died in the battle of the Ark. This memorial honors specifically Master Chief by having the number 117 written on it.

Allusion
A Great Schism occurred in the early Renaissance where there were three popes at the same time, splitting the religion down the middle.

In allusion to the Covenant Civil War, there were 3 major factions in the galaxy vying for total victory: The Humans and their Separatist allies. The San 'Shyuum and the Jiralhanae leading the Loyalists. And the Flood, which took over the Covenant Holy City of High Charity and started to continue what they started on the assimilation of both the warring factions and eventually, the whole Milky Way Galaxy.

Related Links

 * Elites
 * Brutes
 * Prophets