Great Schism

The Great Schism, also known as the Covenant Civil War and the Great Betrayal, was a major conflict between two factions, the Covenant Loyalists and the Separatists, which split apart between October 2552 and November 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 the Flood, which took over the Covenant Holy City of High Charity in an effort to assimilate the other warring factions.

Seeds of Conflict
Even long before the start of the Great Schism, the Prophet of Truth had plans of replacing the Sangheili with the Jiralhanae, as he saw them as more willing and unquestioning pawns, while he despised the Sangheili, doubting their reliability and loyalty. However, he kept these schemes strictly to himself, and waited until the time was right. After Truth learned the location of the Human homeworld, he secretly amassed a fleet of over five hundred warships, entirely commanded by the Jiralhanae, at the command-and-control station Unyielding Hierophant. However, this station and fleet was destroyed by a group of SPARTAN-IIs who learned of its purpose; putting a temporary halt to Truth's plan.

Soon after, the Prophet of Regret made a move 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, and gave his Jiralhanae troops orders to forcibly overtake the Sangheili in command of the remaining forces on and above Earth. When Regret retreated from Earth, his Sangheili-led ships in orbit still continued to engage the UNSC, but now without a leader. Only moments after, the Jiralhanae forces within the fleet and on the ground killed any remaining Sangheili forces, as Truth had ordered. They continued to hold New Mombasa until the reinforcements sent by Truth arrived. As High Charity and rest of the Covenant fleet were now on their way to the newly-discovered Delta Halo, Truth's move remained a secret from the rest of the Covenant. Regret, who would arrive at Delta Halo some time before High Charity and the rest of the Covenant, would serve yet another purpose for Truth; the final stage in his plan.

Conflict Erupts
After the Prophet of Regret was killed by Master Chief, the two remaining Prophets, most notably the High Prophet of Truth, reorganized Covenant society, seeing that the Elites could no longer protect the Prophets due to Regret's death, they replaced 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.

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. Truth also freed all of the Brute prisoners and pardoned them after release (Seen on the Halo Timeline Edict of the High Prophet of Truth). 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, Grunts and some Hunters. Separatists included Elites, with most Hunters and an unknown number of Grunts also breaking away initially. 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).

Sangheili-Human Alliance
The shaky alliance between the Separatists and their former foes, the Humans, was forged entirely out of necessity. The UNSC forces were 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 Delta Halo and firing the Halo Array, which would have killed every sentient being in the galaxy, including himself and the rest of his race, while he, and the rest of the Covenant Loyalist's, still believed the array would only start the Great Journey. However, the Arbiter persuaded the rest of the Sangheili to join the humans. While the two factions experience some friction because their alliance is based on the the enemies of my enemies are my friends concept instead of good political relationships 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 devastated UNSC Fleet in Earth's space were glad to accept the help of the superior Separatist Warships. The Elites' understanding of enemy equipment and Covenant's combat tactics proved invaluable in the Battle of Installation 00, where a fleet three times larger than that sent by the Elites was completely destroyed by the smaller force. Recurrently the heroes of battle, the Arbiter and the Master Chief fought alongside one another many times in the desperate and long conflict. Together the two made an incredible team and the Prophet of Truth was finally killed by the Arbiter with the Master Chief deactivating the Halo Array. Later, the Chief destroyed the Flood-controlled High Charity and the Ark was destroyed when he fired the new Halo ring created above the Ark which also destroyed the Flood. Unfortunatly, the Master Chief and his AI friend and companion Cortana ended up lost in space. The Arbiter's presence at memorial services for the Master Chief indicated that in the wake of victory, Separatists and humans remained friendly to one another as they both had made tremendous sacrifices in order to stop Truth and the Loyalist forces, as well as the Gravemind and the Flood.

With Truth dead, High Charity destroyed, and the Ark essentially lost to the reborn Installation 04's firing, the remaining Loyalist forces remained active in at least some form, rebuilding their tattered strength to continue their war of conquest. Even though the Brutes eventually collapsed into various civil wars, they still posed enough of a threat that Elite 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.

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, if any, 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.

2552
September 22: October 20: October 21st: November 2: November 2-3: November 3: November 8, 2552: November 17, 2552:
 * 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.
 * Thel 'Vadamee, 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".
 * Start of the Battle of Earth. The defeated High Prophet of Regret is forced to retreat to Installation 05, pursued by the UNSC In Amber Clad.
 * Moments after Regret's withdrawal, Jiralhanae within the Covenant forces quickly kill all Sangheili and seize control of the Covenant forces on Earth.
 * 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.
 * Jiralhanae-led reinforcement fleet arrives to Earth and starts the excavation of the Portal.
 * 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 murdered by the Brutes.
 * The Prophet of Truth transfers command of the Covenant Navy to the Brutes, causing the Elites to revolt. Tartarus declares war on the Elites, and the Battle of High Charity begins. Fighting between Elite and Brute forces breaks out all over High Charity. 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 by jumping through Slipspace in the In Amber Clad into High Charity and then afterward through the use of Pelicans to invade the rest of the city.
 * Tartarus attempts to activate Halo.
 * Thel 'Vadamee, with the help of Sergeant Johnson and Rtas 'Vadumee, kills Tartarus.
 * Miranda Keyes aborts the activation of Halo, placing the entire Halo Array on standby status. 343 Guilty Spark reveals the existence of The Ark.
 * 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 departs High Charity for Earth aboard the Forerunner Dreadnought, to join the 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.
 * The Forerunner Dreadnought arrives in the Solar System, and proceeds on course towards Earth at near-relativistic speeds.
 * The Forerunner Dreadnought enters Earth's atmosphere, and John-117 bails out, landing in the jungles near Mount Kilimanjaro.
 * Battle of Voi. The Flood infested Voi, only to be contained by the Fleet of Retribution.

Late November through December, 2552
 * Battle of Installation 00.
 * All Loyalist vessels destroyed over the Ark by the Separatist Fleet.
 * The final Covenant religious leader, the Prophet of Truth, is executed by Thel 'Vadam with help from the Flood. The Master Chief stops the Ark from firing the Halo Rings.
 * High Charity is destroyed by the Master Chief after he overloads the city's main reactors causing them to detonate.
 * Rtas 'Vadum evacuates all humans and Sangheili via the Shadow of Intent, back to Earth.
 * The Battle of Installation 04 (II). Thel 'Vadam, Master Chief and Johnson battle to the control room of Installation 04 (II). Guilty Spark runs rampant, killing Johnson before being subsequently destroyed by John-117. Installation 04(II)'s Sentinels turned on the Master Chief, Thel 'Vadam, and the Elites. The unfinished Installation 04 is activated, damaging the Ark and destroying the entire local Flood infestation including the Gravemind. These final events ended The Human-Covenant War.
 * The Master Chief, Cortana, and Thel 'Vadam escape but only Thel 'Vadam gets back to Earth. The Master Chief and Cortana are drifting in space due to the portal closing. They are inside the back half of Forward Unto Dawn, and while technically MIA, are presumed KIA by the UNSC.

2553
March 3:
 * The Humans and the Elites make a memorial near Mt. Kilimanjaro on planet Earth to commemorate those who were lost in the Battle of the Ark, while also serving as a small memorial for those lost in the Human-Covenant war. The memorial has the number 117 engraved on it in the corner.

2559

 * The Great Schism rages on. While the Jiralhanae wage their own internecine wars, the Sangheili themselves are gradually losing their fleets in a war of attrition, having lost the technical expertise kept exclusively by the Prophets.
 * A Sangheili Shipmaster returns to the partially-glassed human colony of Kholo.

Trivia

 * The term "Great Schism" is taken from human 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.
 * In Contact Harvest the Prophet of Truth foreshadows the Schism, noting that if the Elites ever separated from the Covenant that the entire government would collapse.
 * In Halo 3: ODST, it is implied that the Office of Naval Intelligence was aware of the Great Schism from early on. During the level Tayari Plaza which takes place on October 20, Buck asks Dare about the Elite bodies lying around the city, as they appear to have been killed by the Brutes, to which Dare only responds with it being classified.