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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 October 2552. During the Covenant Civil War, three major factions fought for victory: Humans and their Separatist allies, Covenant Loyalists led by the San 'Shyuum and the Jiralhanae, and Gravemind and the Flood, which took over the Covenant Holy City of High Charity in an effort to assimilate the other warring factions.
The Term "Great Schism" is taken from religious debates over orthodoxy and power, most notably the East-West Schism, the Western Schism, and the Old Believers Schism. The Sunni-Shia split is also often called a Schism.
After the Prophet of Regret was killed by the Master Chief, the two remaining Prophets, most notably the High Prophet of Truth, reorganized Covenant society, replacing the Elites with the Brutes as the Prophets' protectors. The Elites viewed this as a violation of the principle that the Covenant had been founded upon and threatened to resign from the High Council. They also argued that if Truth had not withdrawn the Phantoms that had been en route to Regret's location, the Prophet's death would have been prevented and the Demon would have been killed instead of the Prophet.
However, Truth further demoted the Elites by giving command of their Covenant Fleets to the Brutes. Once enough Brutes were in place, Truth instigated the war by secretly ordering the assassination of many ruling Elites. This was disguised as a Brute insurrection against the Covenant to the Elites, the Hunters and most Grunts. Loyalist factions were led to believe it was an Elite revolt. After the killing of the Elite Council members, war broke out on High Charity, the two sides polarizing quickly. However, this was at first a debate over orthodoxy and leadership. The true split occurred when the Elites learned the truth about the Halos and the Great Journey. Their disillusionment changed their goal from reforming the purity of the Covenant to actively fighting against it.
The split was not cleanly divided by either race or faction. Loyalists followed the Prophets and included Brutes, Jackals, Drones, some Grunts and some Hunters. Separatists included Elites, with most Hunters and many Grunts also breaking away initially. The Great Schism seemed to be more associated with intellect. The Elites' reasoning, logic and good intentions allowed them to see through the abuse of religious authority enforced by the Prophets. The less intelligent and cowardly Grunts' allegiance, however, eventually turned and remained with the Covenant, though there is another possible explanation for the Grunts' shift in allegiance.
It's possible that the only Grunts who actually remained loyal to the Prophets were the most devout followers of the Covenant religion (ex. Deacons). This might also suggest that the Grunts' "new found courage" in Halo 3 might have been the result of fanaticism rather than cowardice. There is some evidence to support this since there are a number of Grunts who commit acts that are anything but cowardly (ex. Kamikaze Grunts). It's also possible that the reason Separatist Grunts are never seen in Halo 3 is that shortly after the Great Schism, they returned to Balaho to lead an uprising against the Deacons and other Loyalist forces. The Separatist Hunters might have done the same on Te, but it is still unknown.
The shaky-to-steady alliance between the Separatists and their former foes, the Humans, was forged entirely out of necessity. The UNSC forces were small, on the defensive, and they had two common enemies that wished for their extinction: the Covenant and the Flood. The alliance of circumstance was forged in the control room of Delta Halo, when Johnson and the Arbiter were coerced to unite in order to prevent Tartarus activating the Halo, which would have killed everything (Brutes included, though the Brutes believed that it was only the Great Journey). However, the Arbiter persuaded the rest of the Sangheili to join the Humans. While the two factions experience some friction, they learn to work with one another for their mutual survival. During the events of Halo 3, the Elites fight alongside Humans in battle. The elites decided to save the humans from destruction.
The devastated UNSC Fleet in Earth's space were unsteadily glad to accept the help of the superior Separatist Warships. The Elites' understanding of enemy equipment and Covenant's frequent combat tactics proved invaluable in the Battle of Installation 00. Recurrently the heroes of battle, the Arbiter and Master Chief fought alongside one another many times in the desperate and long conflict. The Arbiter's presence at memorial services for the Master Chief indicated that in the wake of victory, Separatist and Human forces remained friendly to one another. As they both had made tremendous sacrifices in order to stop Truth and the Loyalist forces. The Elites and Humans will probably continue to be allies and will benefit greatly from being allies with one another in the future.
With Truth dead, High Charity destroyed, and the Ark essentially lost to the reborn Installation 04's firing, it is unknown what exactly the remaining Loyalist forces did. 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 remained a mystery. Ship Master Rtas 'Vadum stated that Truth's Fleet was destroyed. Had any of the Covenant survived on the Ark or in the ruins of their Fleet, they were either taken by the Flood or killed when the unfinished Installation 04 (II) fired and destroyed itself and heavily damaged the Ark. At the end cutscene of Halo 3, victorious Elites depart for their homeworld. With the Covenant disbanded and the Flood threat ended, each race returned home to rebuild their homeworld.
- 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 trialed 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 Spec Ops Commander, Rtas 'Vadumee lead a team of Spec Ops 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 Dreadnought to Earth, to join The Second Battle of Earth. The Brute forces there are already engaged in fighting with the UNSC. Unbeknown 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 escalate 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. He then assumes command of the ship, the Incorruptible, and becomes the de facto leader of the Second Fleet of Homogeneous Clarity. He leads his new 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 Nar '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 moments after Mantakree's forces leave, the survivors joining Mantakree at Onyx.
March 3 The Humans and the Elites make a memorial to commemorate those who were lost in the battle of the Ark. This memorial honors specifically Master Chief by having the number 117 engraved on it.
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