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The Human Downfall
The Human-Covenant war was now in full swing after the destruction of Harvest and its subsequent colonisation by the Covenant Empire. While many humans escaped the partially glassed planet, the effort to retake the planet led to a pyrrhic UNSC victory; although the Covenant Empire claimed victory as well. A large UNSC fleet arrived at Harvest and only after immense human bloodshed (13 UNSC ships destroyed) were the humans able to destroy one Covenant ship.
The Covenant continued to attack and destroy Humans wherever they were found, using their Luminaries to find human worlds. Though the UNSC forces fought bravely, inferior technology made any victory difficult - dependent on strategic and numerical superiority, often with the aid of Spartans. Human armour, missiles, magnetic accelerator cannons, and crude slipspace technology were asymmetrically matched with Covenant energy shields, plasma torpedoes, energy projectors, and pinpoint slipspace jumps. The Covenant, fighting a war of extermination, did not need to commit to full ground invasions except in special circumstances. Covenant ships needed only to destroy human space-borne defences, then reduce the planet's surface to glass with orbital plasma bombardments. Covenant troops were used to soften up UNSC ground forces, or hunt for holy relics. Over twenty-seven years, the Covenant whittled UNSC forces away through firepower and attrition.
Humanity was losing the war, not only were they suffering tremendous losses in life and material, the moral was very low. Human opposition, while sometimes victorious, was overall overwhelmed. One notable exception to the otherwise one-sided fighting was during the Battle of Sigma Octanus IV, where then-Commander Jacob Keyes performed a manoeuvre later dubbed the Keyes Loop; this one manoeuvre proved a great morale boost.
This morale boost did not prevent the Covenant to reach deep into the Inner Colonies and discover and attack the planet Reach. It was in the Battle of Sigma Octanus IV that a Covenant tracking device made its way on board the UNSC Iroquios, which led the Covenant to Reach. The Battle of Reach was a short event, lasting little under a week, but was a massive loss to the UNSC. While they were able to destroy over 262 Covenant ships, the battle ended with a partially glassed Reach and with only a few human survivors.
During the battle a single ship managed to launch and evade from the planet and travel to slipspace while Reach was under heavy bombardment. This ship, captained by Jacob Keyes, of the infamous Keyes Loop, used coordinates taken by the AI Cortana from the battlefield to travel to a location. This location turned out to be a massive Forerunner structure, designated Installation 04.
A Ringworld with an Ancient Enemy
The battle that followed proved to be instrumental to the future of the Human-Covenant war. After the Autumn arrived at the ringworld and some initial fighting, the single human ship crash-landed on the ring. With attacks from both sides, the human and Covenant forces decided it was best to form up into squads and attack the enemy in stealth. One of these Covenant squads had entered a Forerunner structure, in the hope of finding superior Forerunner firearms to kill the enemy. But what they found instead was a Flood containment facility hosting live Flood spores. Soon after accidentally releasing the Flood, the Covenant forces were massacred and forced to lock down the facility.
Later, Captain Jacob Keyes, in desperate need of weapons to arm his troops for their potentially long guerrilla war, went to the facility with Avery Johnson and a part of Fire Team Charlie- previous interrogation of a Sangheili named 'Qualomee had led them to believe it was a weapons cache. Meanwhile, the human Spartan John-117 was underground looking for a way to destroy the ringworld. It was his, and his AI companion Cortana's, idea that only this would be effective against the Flood outbreak. Making his was to the installation's Control Room, the Spartan ran into much Covenant resistance. After many skirmishes with the Covenant, the Spartan was finally able to reach the Control Room and insert Cortana. She notified him of the disastrous events that had evolved elsewhere and quickly sent him to stop Jacob Keyes from opening the flood containment facility. After losing two Marines, the first squad, together with Jacob and Avery, continued until they found a locked door; one of the entry ways locked down by the Covenant forces trapped inside. Upon opening the door, they released the infection. All team members were directly infected by the Flood except for Bisenti and Avery. Avery was only saved because of the Spartan-I augmentations earlier in his career and Bisenti was able to hold of the Flood for a time.
With the Flood now released, the entire battle changed. Now no longer focused on just each other, some (brief) human-Covenant alliances were made to get rid of the invading parasite. But while some alliances were made, others were still in a desperate fight for survival. Under the leadership of First Lieutenant Melissa McKay, human forces staged a raid on the crashed Pillar of Autumn, in order to gain extra supplies of rations, weapons, ammunition, and fuel. They succeeded in destroying a large force of Covenant vehicles and troops. The assault group successfully retrieved a large squad of Warthogs, trailers and four Scorpion tanks from the cruiser's vehicle bays and drove them in a convoy to Alpha Base. At a trio of hills, the Covenant attempted to ambush the humans with a strong force of Wraith mortar tanks, Banshees and Ghosts. Despite the size of the attack, the Covenant forces only managed to inflict moderate damage before losing the tanks and a large portion of their ground forces to the Scorpions' return fire. Back at Alpha Base, a Covenant Spec Ops team accompanied by more Covenant troops ran into a Marine ambush in which all members of both sides were killed other than the Sangheili Zuka 'Zamamee and the Unggoy Yayap. By this time, however, the Covenant ground assault was in full retreat. Zuka 'Zamamee and Yayap were the only known Covenant survivors. They later fled the battle in a recaptured Banshee.
All this fighting and subsequent release of the parasite had not gone unnoticed by the installation's Monitor, 343 Guilty Spark. Fearing for the universe if the Flood would be able to spread, he immediately began searching for a suitable 'Reclaimer' (human) who would be able to activate Installation 04's defences. At first, Spark came upon Staff Sergeant Marvin Mobuto who was brought to the Library to retrieve the Activation Index. Even though Marvin showed great skill and perseverance, he was ultimately overwhelmed and killed by the Flood and Spark had to search for another, better equipped, Reclaimer. The second Reclaimer he found was one with more advanced equipment and skill, John-117 was taken to the Library to retrieve the Activation Index. He succeeded, and together with John, Spark teleported to the Control Room. The Monitor explained that activation protocols forbid him from personally uniting the Index with the Core to activate the ring; only a Reclaimer could be permitted to do so. But before the protocol could be completed, Cortana intervened in the activation of the Installation. Cortana explained that the activation of Halo meant the destruction of all sentient life in the vicinity, and the Reclaimer became uncooperative to Spark's requests. With the Activation Index in the hands of a foreign hostile AI, and no Reclaimer present willing to activate the Installation, Spark sent Sentinel Drones to retrieve the Index.
Now the humans had to deal with fighting from 3 different enemies, Covenant, Flood and Forerunner constructs. As the destruction of the ring was not possible with the installation's own function, John-117 made his way to the Pillar of Autumn. The plan was to use the Autumn's engines to blow up the ring, destroying everything and hopefully stopping the spread of the Flood. Halted on many fronts, John-117 finally managed to delayed detonate the engines so he could get away on board a nearby GA-TL1 Longsword-class Interceptor.
The Climb Back To The Top
The loss of the Covenant forces was devastating to the Covenant, but not more than the loss of the Forerunner artefact itself. Branded as the utmost heresy, the Supreme Commander Thel 'Vadamee was stripped of his rank, humiliated, branded with the Mark of Shame and turned into the Arbiter. As the Arbiter, he was to be send to missions from which he was not expected to return. On the other side of the battle, Avery Johnson, John-117 and Jacob Keyes received medals for their outstanding bravery during the battle. It was Miranda Keyes, Jacob Keyes' daughter, who accepted the medal, as Jacob had fallen victim to the Flood and was absorbed by the Proto-Gravemind.
It was during the medal ceremony that Earth was attacked by a small Covenant fleet. The fleet was in search for the the Ark, and was unaware of the large human population. His significantly outnumbered and out-classed fleet was quickly attacked by a fleet of eight Marathon-class heavy cruisers and sixty-seven frigates under the command of Fleet Admiral Harper. As the Solemn Penance was preparing for a slipspace jump, the UNSC In Amber Clad, with John-117, Miranda Keyes and Avery Johnson on board, pursued the ship and together they made it into slipspace.
As they made their way out of slipspace, they discovered another Halo Array, designated Installation 05. After evaluating their situation, Miranda Keyes ordered John-117 to capture and interrogate the Prophet of Regret about the Installation. During their search for the Prophet, Cortana found out that he was planning to detonate the ring and fulfil the Great Journey. But for this the Covenant needed two things, the Activation Index and a Reclaimer to activate it. The Prophet of Truth ordered the Arbiter Thel 'Vadamee to go on the Installation's surface and retrieve the sacred icon (Activation Index) to enable the start of the Great Journey. On the surface, the Arbiter was tasked by the Jiralhanae Chieftain, Tartarus, to shut down the Sentinel Wall to allow Covenant forces to be deployed and assist the cause. When Thel had made his way to the Library, the Arbiter assaulted Miranda Keyes and Avery Johnson. After neutralising the pair, the Arbiter retrieved the Index but was betrayed by the Jiralhanae leader Tartarus.
Thrown into the depths of the Forerunner structure, Thel 'Vadam was taken by the Flood Gravemind and brought to him, together with John-117. Here, the Gravemind was able to convince Thel that the Prophets had lied to him, and the activation of the ring would mean the death to all of them. The Gravemind tasked John and Thel to stop Regret's plan to activate the ring. Thel was able to convince others of the truth he now knew, setting the Great Schism in motion, and John was able to defeat the Prophet.
After the Prophet of Regret was killed by John-117, the two remaining Prophets, most notably the Prophet of Truth, reorganised Covenant society. Saying that the Sangheili could no longer protect the Prophets due to Regret's assassination, they replaced the Sangheili with the Jiralhanae as the Prophets' protectors. The Sangheili viewed this as a violation of the principles 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.
Telling the Covenant forces that the Sangheili were rebelling, the Prophets replaced and assassinated ruling Sangheili. However, the true split occurred when the Separatists 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.
Ending the War
With the Covenant Separatists on their side, humanity's forces were much more successful against the Covenant Loyalists. As the Great Schism was happening, the Prophet of Truth decided to travel to Earth in the Forerunner dreadnought present at the center of High Charity. Just before it could take off, John-117 was able to clamber on it and together they entered slipspace towards Earth.
Truth made his way to the portal to the Ark, located on Earth near the town of Voifrom which he would be able to detonate all the Halo rings at once. After the portal was successfully opened, Truth's entire fleet entered it and made their way to the Ark. The Human-Covenant Separatist alliance quickly followed, but could not stop the Flood-controlled Indulgence of Conviction to join them, which meant that the Ark was now also infected with all the Flood in the universe. Fighting their way through the opposition, John-117 and Thel 'Vadam were able to kill the Prophet of Truth just as he was detonating all the Halo rings.
To prevent anyone from using the Ark in the future to destroy all sentient life in the galaxy John decided to detonate the partially-complete replacement for Installation 04. This would not mean the destruction of the sentient life nearby, but would destroy the Ark and its inhabitants. When Avery Johnson informed the installation's monitor of this plan, he became irate and killed Avery with a quick and powerful laser attack. After John was able to destroy the monitor, he and Thel 'Vadam made their way to the UNSC Forward Unto Dawn which would take them back to Earth. But the Dawn was not fast enough to entirely enter the portal before the Ark exploded and it was cut in half. The front part, housing Thel, made its way safely to Earth, while the rear end, housing John-117 and Cortana, drifted in space, waiting for rescue.
The war had ended, and with it the Covenant Empire. The Arbiter Thel 'Vadam became the de facto leader of the newly formed Swords of Sanghelios and called all Sangheili back to Sanghelios, but not before attending the Hillside Memorial ceremony. John-117 was marked Missing In Action, although presumed dead.