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The Great Schism, also known as the Covenant Schism, was a major civil war between the forces loyal to the Covenant (led by the San'Shyuum and the Jiralhanae) against the Covenant separatists (the Sangheili and their followers), which split apart on November 3, 2552. The High Prophet of Truth ordered the extermination of the entire Sangheili species, forcing them out of the Covenant. Battles during the Schism took place all throughout Covenant space, most prominently on High Charity, the heart of the alien empire. The Flood additionally played a tertiary role, when they took over the holy city in an effort to assimilate the other warring factions. The deciding battles were fought between the Sangheili Fleet of Retribution allied with the UNSC against the High Prophet of Truth and his remnants of the Covenant on the Ark. The Schism marked both the end of the Covenant and the partition of its client species for a thousand years. For the UNSC, it served as a major turning point that led to the end of the war after their disastrous defeat on Reach.
For centuries over the course of the history of the Covenant, various high ranking Sangheili with great influence would use their power to ask questions, eventually coming close to discovering the truth about the Forerunners. Discovering such a truth would falsify the Covenant religion and shatter the empire along with its power structure. As such, the San'Shyuum High Prophets perceived these influential Sangheili as a threat to their authority, and would send them on suicidal missions decorated under the honorary guise of Arbiters to discretely remove their threatening presence.
With this history of troublesome influential Sangheili well documented among the High Prophets, the threat the Sangheili posed was made even more apparent during the Human-Covenant War in 2552, when Sesa 'Refumee's heretic faction spread information about the Great Journey being false. Intending to prevent the Covenant from falling apart and losing power, the High Prophet of Truth made plans to eject the entire Sangheili species from the hegemony, viewing them as untrustworthy and doubting their reliability and loyalty. Supreme Commander Thel 'Vadamee, another powerful and influential Sangheili, failing to prevent the Demon from destroying a holy "Sacred Ring", further perpetuated San'Shyuum distrust toward the Sangheili.
The High Prophet of Truth plotted to eventually replace the Sangheili with the Jiralhanae, as he saw the latter as more willing and unquestioning pawns. Ever since the Jiralhanae's integration in 2492, their dominating physicality and aggressive behavior was perceived as a threat by the Sangheili to their superior status in the Covenant hierarchy. In turn, the Sangheili treated the Jiralhanae poorly and oppressed them, to keep them in line. Competition for dominance in the Covenant military and hatred festered between the two species, though the Sangheili maintained their authority and power as a founding race. Feeding off of their societal rivalry, Truth knew that the Jiralhanae would be more than happy to replace the Sangheili as the Covenant's military leaders. He had appointed Tartarus, a loyal Jiralhanae, to the position of Chieftain of the Jiralhanae who would help him execute his plan. Truth kept these schemes to himself and waited until the time was right to implement them.
After the High Prophet of Truth learned the location of the human homeworld, he secretly amassed a fleet of over five hundred warships, commanded entirely by Jiralhanae, at the command-and-control station Unyielding Hierophant. In September 2552, this station and the fleet were destroyed by Spartan-II Blue Team who learned of its purpose shortly before the invasion could commence. This put a temporary halt to Truth's plans.
On October 20, the High Prophet of Regret made a move the High Prophet of Truth did not expect: having discovered a significant Forerunner artifact on Earth on his own, but unaware of the fact it was humanity's homeworld, he took his fleet of only fifteen ships to Earth. Immediately after Truth learned of this, he sent the remnants of the fleet he had amassed to Earth; he gave his Jiralhanae troops orders to forcibly overtake the Sangheili in command of the remaining forces on and above Earth. To Regret's surprise, Earth was the human homeworld, resulting in a massive battle forcing him to flee. When Regret retreated from Earth, his Sangheili-led ships in orbit and ground forces continued to engage the United Nations Space Command without a leader. Moments after, the Jiralhanae forces within the fleet and on the ground discretely killed all remaining Sangheili on Earth, as Truth had ordered. They took over the Sangheili's duties to occupy the human city of New Mombasa until more Jiralhanae reinforcements sent by Truth arrived. As High Charity and the rest of the Covenant fleet were on their way to the newly discovered Halo Installation 05, Delta Halo, the murder of these Sangheili ground forces remained secret from the rest of the Covenant.
Regret arrived at Delta Halo weeks before High Charity and the rest of the Covenant, and indirectly served yet another purpose for Truth plan: to scapegoat the Sangheili. With the arrival of the UNSC In Amber Clad commanded by Commander Miranda Keyes on Delta Halo, the UNSC managed to assassinate the Prophet of Regret after they got the intel they needed, with Spartan John-117 set to carry out this task.
The Changing of the Guard
After the High Prophet of Regret was killed by the Demon on November 2, 2552, the two remaining Hierarchs reorganized Covenant society. Claiming that the Sangheili could no longer protect the Prophets due to Regret's death, the High Prophet of Truth publicly replaced the Sangheili with the Jiralhanae as the Prophets' protectors. Much to their dismay, all Sangheili Honor Guardsmen were ordered to give away their armor and weapons to the new Jiralhanae Honor Guardsmen. The Sangheili viewed this as a violation of the principle that the Covenant had been founded upon and threatened to resign from the Covenant. Special Operations Commander Rtas 'Vadumee relayed this warning from the Sangheili High Councilors to Truth, who attempted to comfort the situation by calling it a mere "exchange of hats". Several Unggoy and Kig-Yar would join in protest against this change as well.
The High Prophet of Truth further demoted the Sangheili by giving command of their fleets to the Jiralhanae, including the Fleet of Profound Solitude, Fleet of Tranquil Composure and Fleet of Inner Knowledge. Many Sangheili Shipmasters and Fleetmasters would be replaced with new Jiralhanae commanders. Truth allocated more loyal forces to his disposal by pardoning and releasing all Jiralhanae prisoners, while publicly framing it as a celebration for the species newly elevated status in Covenant society.
The Sangheili found these changes to be deeply humiliating, as founding members of the Covenant they were insulted to see their societal status quickly becoming relegated below the Jiralhanae.
The High Prophet of Truth predicted that the High Council would elect a new Hierarch to replace Regret, and so he made his move to eliminate the Sangheili High Councilors to prevent another moderate Prophet from being elected. Once enough Jiralhanae were in place, Truth instigated a pogrom by ordering the assassination of all Sangheili Councilors. Many Sangheili High Councilors and former Honor Guards were ordered to meet in the Control Room of Installation 05 to begin preparing for the Great Journey. However, Jiralhanae Captain Melchus arrived at the Control Room, with a large heavily armed contingent of Jiralhanae, and proceeded to massacre the Councilors and former guardsmen. All Sangheili in the room were killed except for G'torik 'Klemmee who survived a deadly fall and later escaped, the rest were smashed into bloody pieces by gravity hammers. Concurrently, Chieftain of the Jiralhanae Tartarus and his guards attempted to kill Arbiter Thel 'Vadamee in the Library, seizing the Index and knocking him into a deep pit, as ordered by Truth. This would spark the start of the Great Schism.
Word of the massacred Sangheili Councilors immediately spread and was perceived as an insurrection against the Covenant to the Sangheili. The Jiralhanae and other loyalists were led to believe it was a Sangheili revolt, rejecting the Jiralhanae's newly elevated status, and were ordered to exterminate the entire Sangheili species and kill all of them on sight. After the slaughter of the Councilors, war and violence broke out on High Charity, with the two sides polarizing quickly. Video messages of the various massacres were sent to all Sangheili forces, resulting in the entire species learning that they had been forced out of the Covenant. The ships within the High Charity defense fleet began shooting each other down while gunfire erupted aboard the interior of High Charity. At the front lines of the conflict, the species of the Covenant took distinct sides. Those who followed the High Prophets included all San'Shyuum and Jiralhanae (with a few exceptions), many Kig-Yar and Yanme'e, some Unggoy, and a few Mgalekgolo. The forces allied with all the Sangheili consisted of many Mgalekgolo, Unggoy and Huragok.
The Prophet of Exquisite Devotion who had been torturing Sangheili, discovered that the Prophet of Clarity was attempting to aid them. Devotion then attempted to have Clarity executed for treason. However, a group of Sangheili led by G'torik 'Klemmee arrived and rescued the Prophet of Clarity—killing Exquisite Devotion in the process. After the Sangheili-led and Jiralhanae-led forces fought each other in High Charity for several hours, Flood infected Pelicans eventually crashed into the holy city spreading the parasite. Around this time, the High Prophet of Truth left the High Prophet of Mercy to die at the hands of the Flood, solidifying his place as the autocrat of the Covenant. The chaos was further intensified when Truth abandoned High Charity in the Forerunner dreadnought on a journey to Earth, disconnecting it from the grid, leaving the entire city in the dark without power amongst the Flood. Clarity, 'Klemmee, and the rest of their small group would later escape High Charity aboard a stolen supply ship, Journey's Sustenance. High Charity fell to the Flood, leaving the Covenant without a capital and the dying San'Shyuum without a homeworld. Sangheili ships attempted to quarantine the region of space around High Charity, preventing any possibly infected ships from leaving, while also shooting down enemy Jiralhanae ships.
Conflict occurred all across Covenant space, including from within ships themselves. Notably, one Sangheili Shipmaster grabbed the Prophet aboard his ship, having barged into his cabin, and executed him before the rest of the crew. Chol Von, a T'vaoan shipmistress, captured a Phantom, killing two Sangheili in the process. She renamed her missionary ship Joyous Discovery as Paragon.
The civil war was at first a conflict over orthodoxy and leadership, as Imperial Admiral Xytan 'Jar Wattinree summoned many Sangheili to Joyous Exultation in a plot to wipe out the Jiralhanae. However, a revelation among the Sangheili occurred when Thel 'Vadam's contingent discovered the truth that the Halos would kill all life in the galaxy and that the Great Journey was a lie, from both the Gravemind and 343 Guilty Spark. Their disillusionment changed their goal from reforming the purity of the Covenant to actively standing against the Covenant religion the following day. Wattinree's separatist forces would be destroyed in the meantime in the accidental NOVA bombing of Joyous Exultation and the Onyx Conflict.
On Installation 05, Sergeant Major Avery Johnson's Marines met Arbiter Thel 'Vadam's forces and united to prevent the Chieftain of the Jiralhanae, Tartarus, from activating Delta Halo and firing the Halo Array. The Arbiter fought Tartarus face to face, while Johnson picked away at the Jiralhanae's shields with a beam rifle from afar. After killing Tartarus, the Arbiter solidified this alliance of circumstance by bringing in all local Sangheili forces to side with Commander Miranda Keyes and the UNSC. A shaky alliance between these Sangheili and their former foes, the humans, was forged out of necessity and revenge against the Covenant to some extent. Both sides had two common enemies that wished for their extinction: the Covenant and the Flood. Meanwhile, Rtas 'Vadum led a strike team of Sangheili to capture the Shadow of Intent from the Jiralhanae as a flagship for their local forces, forming the Fleet of Retribution.
The Fleet of Retribution stayed behind on Delta Halo to quarantine the Flood outbreak by glassing the surface, while the Arbiter joined the UNSC forces back to Earth to chase the High Prophet of Truth. Truth was excavating the Forerunner artifact on Earth that Regret had discovered nearly a month prior and was seeking to use it to travel to the Ark to fire all the Halo rings. Weeks later on November 17, the devastated UNSC Home Fleet attempted a last-ditch assault on Truth's Forerunner Dreadnought, which had integrated with portal artifact. This attack failed while a Flood-controlled battlecruiser crashed in Voi only moments after Truth's Dreadnaught and the rest of his fleet entered the portal generated by the artifact.
The Sangheili Fleet of Retribution, led by Shipmaster Rtas 'Vadum, arrived at Earth in pursuit of the Flood infested cruiser. Several Sangheili were deployed to assist the UNSC forces in containing the Flood in Voi from spreading across the entire planet. After the allied forces were airborne, the Fleet of Retribution glassed the city and its environs under the order of Shipmaster 'Vadum, Arbiter Thel 'Vadam had persuaded him that only glassing the local area was necessary opposed the the whole planet. This led to a debate between Shipmaster 'Vadum and Fleet Admiral Lord Terrence Hood. The Sangheili and Commander Miranda Keyes' forces agreed to follow Truth to the Ark beyond the portal.
The joint Sangheili-UNSC fleet arrived at the Halo Array's control center, Ark Installation 00, on December 11 where they engaged Truth's fleet. During the ensuing conflict, the Fleet of Retribution completely destroyed their Jiralhanae counterpart in the space battle, despite the latter's three-to-one numerical superiority.
Sangheili ground forces were later deployed to the final battle of the war, riding in green colored Ru'swum-pattern Phantoms to match the UNSC, and helped Spartan John-117 disable the shield generators protecting the installation's Citadel where the High Prophet of Truth was hiding. As the Sangheili forces killed many Jiralhanae, John-117 and Arbiter Thel 'Vadam entered the Citadel and fought through what remained of Truth's personal guard. Truth desperately communicated holographic messages to his followers, blaming the heretics and the parasite. After reaching the control panel the Arbiter discovered that the Hierarch had been infected by the Flood; as the High Prophet slipped in and out of lucidity, 'Vadam exchanged a few words with him before stabbing him through the back with his Energy Sword. The High Prophet of Truth and his forces were dead, effectively dissolving the Covenant.
With the war over, Shipmaster 'Vadum evacuated the remaining Sangheili and human forces aboard his flagship, the Shadow of Intent, and left Master Chief John-117 and the Arbiter behind to deal with the Flood at their request. Any remaining Covenant forces were presumed to be killed when Halo Installation 08 was activated and the Ark was severely damaged by the debris; though a few remnants held out in the Anodyne Spirit and had miraculously managed survived even years after the war. The firing of the incomplete ring had also ended the threat of the Flood. The Master Chief, the Arbiter, and the AI Cortana had escaped on the frigate UNSC Forward Unto Dawn, which was split in half when their escape portal closed too early.
With Truth dead, High Charity destroyed, and the Ark heavily damaged after Installation 08's firing, some of the remaining Jiralhanae forces tried to rebuild their tattered strength to continue their war of conquest. The San'Shyuum eventually abandoned them to hide from the vengeful wrath of the Sangheili, as the Jiralhanae collapsed into various civil wars. The Jiralhanae resorted to raiding Sangheili settlements, plundering resources for survival. Some Sangheili commanders kept up the offensive against them for at least another six years, even as they continued to lose irreplaceable warships and the war continued with no end in sight.
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