From Halopedia, the Halo wiki
The Great Schism, also known as the Covenant Schism, or the Great Betrayal among the Sangheili, was a major civil war between the forces loyal to the Covenant against the Covenant separatists, which split apart on November 3, 2552. During the Schism, three major factions fought for victory: the Sangheili Fleet of Retribution allied with the UNSC; the remnants of the Covenant led by the San'Shyuum and the Jiralhanae; and the Flood, which took over the Covenant holy city of High Charity in an effort to assimilate the other warring factions. 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 eventually come close to discovering the truth about the Forerunners, which would falsify the Covenant religion. Such influential Sangheili were perceived by the High Prophets as a threat to their authority and power, and they would send these Sangheili on suicidal missions as newly appointed Arbiters to discretely remove their threatening presence.
With this history of influential Sangheili well documented among the High Prophets, the threat the Sangheili posed was made even more apparent 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's failure to prevent Demon John-117 from destroying a holy "Sacred Ring", was another example of a powerful and influential Sangheili committing questionable actions, which further perpetuated distrust. Truth would eventually replace the Sangheili with the Jiralhanae, as he saw the latter as more willing and unquestioning pawns. He had appointed Tartarus, a loyal Jiralhanae, to the position of Chieftain of the Jiralhanae who would help him execute his plan. Feeding off the societal rivalry between the Sangheili and Jiralhanae, Truth knew that Tartarus and the Jiralhanae would be more than happy to replace the Sangheili as the Covenant's military leaders. Truth kept these schemes strictly to himself and waited until the time was right to implement them. After 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 a group of SPARTAN-IIs 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 a fleet of 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, but now without a leader. Only moments after, the Jiralhanae forces within the fleet and on the ground 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 now on their way to the newly discovered Halo Installation 05, Truth's scheme remained secret from the rest of the Covenant. Regret, who would arrive at Delta Halo weeks before High Charity and the rest of the Covenant, would serve yet another purpose for Truth: the final stage in Truth's plan. With the arrival of the UNSC In Amber Clad commanded by Commander Miranda Keyes on Installation 05, the UNSC decided to assassinate the Prophet of Regret after they got the intel they needed, with John-117 set to carry out this task.
The Changing of the Guard
After the High Prophet of Regret was killed by Spartan John-117 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. 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 used to having a higher societal status than 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 many 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. This would spark the start of the Great Schism.
This massacre of the Sangheili Councilors was perceived as an insurrection against the Covenant to the Sangheili, as well as many Mgalekgolo and Unggoy. The Jiralhanae and other loyalists were led to believe it was a Sangheili revolt. After the assassination 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 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), most Kig-Yar and Yanme'e, few Unggoy, and a minority of the Mgalekgolo. The forces allied with the Sangheili consisted of many Mgalekgolo, Unggoy and Huragok.
Chol Von, a T'vaoan shipmistress, renamed her missionary ship Joyous Discovery as Paragon at some point of the Great Schism. During the Schism, she captured a Phantom, killing two Sangheili in the process. After discovering that the Prophet of Clarity was attempting to aid the Sangheili, the Prophet of Exquisite Devotion attempted to have him executed for treason. However, a group of Sangheili led by G'torik 'Klemmee arrived and rescued the Prophet of Clarity—resulting in the death of Exquisite Devotion in the process. The group would later escape High Charity aboard a stolen supply ship, Journey's Sustenance.
The civil war was at first a conflict over orthodoxy and leadership, however the true split occurred when Thel 'Vadam's contingent of Sangheili, the Fleet of Retribution, discovered the truth about the Halos and the Great Journey. Their disillusionment changed their goal from reforming the purity of the Covenant to actively standing against the Covenant religion the following day. Around this time, 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 shaky alliance between the Sangheili Fleet of Retribution 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. This alliance of circumstance was forged in the control room of Installation 05, when Sergeant Major Avery Johnson and Arbiter Thel 'Vadamee united to prevent the Chieftain of the Jiralhanae, Tartarus, from activating Delta Halo and firing the Halo Array. After succeeding in killing Tartarus, the Arbiter persuaded many Sangheili to ally with the humans, forming the Fleet of Retribution.
On November 17, the devastated UNSC Home Fleet attempted a last-ditch assault on the High Prophet of Truth's Forerunner Dreadnought, which had integrated with the Forerunner artifact that Regret had discovered nearly a month prior. This attack failed and a Flood-controlled battlecruiser crashed in Voi only moments after Truth's fleet entered the portal generated by the artifact. However, the Sangheili Fleet of Retribution, led by Shipmaster Rtas 'Vadum, arrived in pursuit of the cruiser; as the fleet glassed the city and its environs, the Sangheili and UNSC agreed to follow Truth beyond the portal.
The joint Sangheili-UNSC fleet arrived at the Halo Array's control center, Installation 00, on December 11. During the ensuing battle, the Fleet of Retribution completely destroyed their Jiralhanae counterpart, despite the latter's three-to-one numerical superiority. Sangheili forces later helped SPARTAN-117 disable the shield generators protecting the installation's Citadel, in which the Prophet of Truth was hiding. Master Chief John-117 and Arbiter Thel 'Vadam entered the Citadel and fought through what remained of Truth's personal guard. After reaching the control panel they discovered that the Hierarch had been infected by the Flood; as the Prophet slipped in and out of lucidity, 'Vadam stabbed him in the back. The Flood-controlled High Charity was destroyed shortly thereafter, effectively dissolving the Covenant.
Shipmaster 'Vadum evacuated the remaining Sangheili and human forces after the holy city's destruction. Seemingly, only his flagship, Shadow of Intent, remained. Any remaining Covenant forces were killed when Halo Installation 08 was activated and the Ark was severely damaged by the debris; the activation also ended the immediate 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.
After the Human-Covenant War
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. Even though the Jiralhanae eventually collapsed into various civil wars, they still posed enough of a threat that 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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