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The ORION Project and its evolution

 
Sometime in the future, the United Nations Space Command ( UNSC) had led humanity to colonize several planets around the galaxy thanks to the invention of the Shaw-Fujikawa Translight Engine that allows human-built spaceships to enter a "slipstream" in space where faster-than-light travel is possible. However, in the early 25th Century, tensions escalated between the human colonists of the more stable and populous "Inner Colonies" and the fringe worlds of the "Outer Colonies." As the amount of colonized planets grew, the Outer Colonies began to question the policies of the UNSC and the United Earth Government and whether they truly applied to them all the way out in space. This eventually led to a civil war between them. 
 
The UNSC and their secretive Office of Naval Intelligence (ONI) drafted Dr. Catherine Halsey along with other top scientists to start the ORION Project which would later become known as the SPARTAN-I Project. The Spartans that were successfully created from volunteer military men and women were genetically modified supersoldiers who were tasked with suppressing the insurrection from the secessionists in the Outer Colonies.
 
In 2517, the secessionists grew too numerous for a small number of Spartans to handle alone, and the need for a larger number of them was necessary, so the SPARTAN-II program was created to quickly create a larger number of prime supersoldier candidates. These new Spartans were drafted from a certain genetic type of human before they hit puberty and injected with a load of genetic modifications to rapidly build up their strength, speed and intelligence beyond that of the average human. On top of that, a new exoskeleton was developed that would augment their already-increased abilities in Project MJOLNIR. 75 children were kidnapped by ONI for this experiment and smuggled onto the colony world of Reach for training. By the end of training, only 33 survived the SPARTAN-II program and became fully-functional Spartans.
 

The Sangheili join the Covenant

Around the 9th Century BCE, the planet of Sanghelios was visited by the beings known only as the " Forerunners" who had gifted them with certain technology. However, the Sangheili (currently called "Elites" by the humans) considered these objects sacred items gifted to them by gods, and refused to touch them. Several years later, the Sangheili were visted at their home planet by another alien race, the San 'Shyuum (later called "Prophets" by the UNSC) who had also been gifted technology by the Forerunners. Unlike the Sangheili, the San 'Shyuum had no taboo about using the Forerunner technology to advance their own, and the two races fought each other over whether or not it was allowed to use such technology gifted by the gods. 
 
 Artist's rendition of ancient Sanghelios
 
The Sangheili had greater numbers, but they were initially decimated by the Keyship and the superior technology that the San 'Shyuum wielded until the Sangheili finally broke their own taboo and made use of their own Forerunner-gifted technology to fight back. By 876 BCE, the two sides signed an uneasy truce with each other that would expand around 852 BCE into what is currently known as The Covenant
 
The Prophets offered a spiritual awakening and unity to the Covenant, promising that with their help they would search the galaxy for Holy Rings (the titular Halo structures) and activate them to begin the Great Journey that would provide eternal salvation for those who believed in the gods. The Elites became the dominant military muscle within the Covenant and were nearly equal with the Prophets in terms of technological advances, having adapted some of the Prophets beliefs to their own belief system. The Elites' feudalistic society somehow allowed medical and technological advancement while keeping a stable power structure in place.
 

The SPARTANS face a new, deadlier threat

Sometime during 2525 AD, the Covenant came to the human colony world of Harvest in the first recorded meeting between the two sides. The human colonists and ONI originally thought their ships were being raided by secessionists, but it soon turned out that strange aliens were behind the raids on their ships. The Covenant, for their part, had come to Harvest seeking Forerunner "relics" and demanded that the humans hand them over, though the humans had no clue what relics they were searching for. The two sides initially tried to negotiate a peace agreement, but an overeager Grunt attacked a member of the colonial militia and ended up provoking hostilities with the human colonists there. The First Battle of Harvest began, and ended with the Covenant partially glassing the planet as some of the colonists tried to escape.
 
A Spartan prepares to hold a bridge against several Elites.
After receiving news of the new alien threat from the Covenant, ONI sped up Project MJOLNIR and began training the Spartans to combat this greater threat to humanity than mere human secessionists. Despite their dwindling numbers, the SPARTAN-II project led to a few successful rearguard actions against the Covenant, helped in part by ONI's propaganda campaign to paint the Spartans as legendary soldiers who were incapable of dying and could take on entire armies by themselves. Any Spartans who were killed were only listed as MIA or WIA (Missing or Wounded In Action, respectively) to preserve this legend. In 2547, some of the SPARTAN program was revealed to the public in order to increase morale on the human front, which it did. However, the Covenant still maintained a slight technological advantage and continued pushing the humans out of their colonial worlds.
 
 John-117 on Reach
Later, in 2552, several Spartans gathered on Reach for a plan that the UNSC's Naval High Command came up with to quickly end the war: A surgical strike that would involve capturing a Covenant ship, infiltrating the Covenant fleet near their homeworld, and holding the Covenant leadership hostage until they agreed to a ceasefire. However, the Covenant attacked the colony of Reach before High Command could start their plan, slaughtering or wounding several of the surviving members of the SPARTAN-II program. One of those members, John-117, managed to fight his way out and was rescued by the Halcyon-class UNSC cruiser called the Pillar of Autumn and was placed in cryostasis. 
 
However, his rest was short-lived when the ship was attacked by Covenant forces anyway, and he ended up landing on Halo Installation 04 with other surviving Marines. John-117 single-handedly fought through both the Covenant and a new parasitic lifeform known as The Flood in order to eventually destroy the Halo and escape back to UNSC-controlled space.
 

The Elites begin to have doubts

At first, the Covenant Elites followed the lead of the Prophets without question, enjoying the opportunity to destroy the heretics and demons that would not accept the glory of the gods. However, sometime during the fight between Covenant and the Humans, some Elites began questioning their leaders. Despite the fact that humans were physically weaker and more timid to them, the Elites began to question why the Prophets did not even bother trying to show them the error of their ways and offer the humans a place in the Covenant. After all, despite their weakness, some Elites thought that the humans had fought bravely or even honorably against the overwhelming might of the Covenant, a few even considered the humans as equals. 
 
However, the prophets branded any Elites who uttered such thoughts as heretics and traitors to the Covenant, and would send their loyal soldiers to kill the Elites who did not see their word as the truth. The leader of one such group of heretics was later hunted down by the Arbiter Thel 'Vadam and a squad of Elites as a test of loyalty by the Prophets. However, with the death of the Prophet of Regret at the hands of the "Demon" himself (the Spartan named John-117 or "Master Chief"), the remaining Prophets decided to replace their Honor Guard and several leadership positions from the Elites to the Brutes (or "Jiralhanae") instead. On top of this, the Arbiter and his allies learned what Cortana and John-117 found out before: that the activation of the Halo would essentially lead to their own extinction.
 
This led to The Great Schism, where the Elites seceded en masse from the alliance of the Covenant and sided with the Humans instead thanks to the Arbiter's own counsel. Where the Brutes stepped in to fill the gap left by the Elites, the Elites decided to fight against them along with the Prophets and the Flood.
 

The Human-Elite Alliance

 
Having turned their backs of the Prophets and the Covenant, the Elites decided to work together with UNSC forces to kill the Prophet of Truth after the Battle of Earth. Once they had finished that, the Arbiter Thel 'Vadam and the Spartan called Master Chief worked together to end the threat of the Flood once and for all. 
 
Back on Earth, the Arbiter signaled to UNSC Fleet Admiral Lord Terrence Hood that their two races would be at peace, as the Master Chief had sacrificed himself to stop the Flood and was considered MIA. However, when the Elites returned to their homeworld, they not only had to deal with the anger of the surviving Covenant forces, but yet another rift within their own society over whether or not they should have turned against the Prophets.

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