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Ancient humanity had been around for a very long time, tracing its roots to more than 1.1 million years ago. In this prehistoric time, humanity consisted of many species of the genus Homo living on Erde-Tyrene, coexisting in peace. After many achievements in technology, humanity reached Technology Tier 2 and were beginning to settle colonies on numerous world along the galactic margin.
But due to still unknown reasons, this civilisation collapsed, perhaps multiple times, until they did not know their own history. They lost most of their records, including that Erde-Tyrene was their original homeworld. When humanity had once again reached Tier 2 after tens of thousands of years, they visited many alien worlds, and discovered human ruins on a great many worlds. Having settled on the Precursor world Charum Hakkor, many believed that to be their original homeworld. It was not until a science group led by Yprin Yprikushma that humanity learned that Erde-Tyrene was their birth ground. This was led by much opposition, with Forthencho being the chief opposition. He and others believed the homeworld lay elsewhere, on a planet with much more human artefacts.
Somewhere during this time, humanity made contact with the San'Shyuum, which would lead into a alliance. They regularly traded produce, items, and technology with each other. One such example is the Pheru, an animal domesticated and used as a pet. They would also join their military strength when needed.
Then, ancient humanity made contact with the Forerunners, the most advanced alien lifeforms they had encountered. Having achieved a great technologically society, they were still inferior to the Forerunners. Not only that, because the Forerunners had been around that much longer, they held much greater power in the galaxy, something that was a source of contempt among humans. As they were looking to escape from the Forerunners dominion, humanity expanded in the opposite direction, among the Orion Arm. This caused their technology level to rise, until the Forerunners considered them the second greatest military power and greatest rival to date.
By collecting and reverse-engineering Precursor technology at Charum Hakkor, one of the largest collections in the galaxy, humanity's rapid technological achievements made willing challenges towards Forerunner policies. This, coupled with their belief that they - not the Forerunners - were the true inheritors of the Mantle of Responsibility from the Precursors, made them ideological enemies, and heretics from a Forerunner perspective. When Humanity annihilated 50 defenceless systems in which Forerunners had resettled other species during the war, that was the last straw. After displacing the indigenous populations of those systems, Humanity replaced them with human colonies to strengthen their hold over these new territories.
The Battle and the Flood
For a more detailed story about the Flood, please see Halo101: Flood
The battle would rage on for about 1,000 years, with heavy losses on both sides. Colonising many alien worlds, the humans eventually stumbled upon an automated cargo ship filled with millions of small transparent cylinders filled with an unknown powder. Determining that it was send from the Large Magellanic Cloud, humans began to test the powder. Early tests showed that the powder was harmless and useless, consisting of lifeless short-chain organic molecules. As they seemed to instil more favourable behaviour in their Pheru, the powder became coveted and expensive.
It was not until several centuries later that the mutations started to happen. Pheru were beginning to grow fleshy growths from their body, while others suffered physiological damage. Those with fleshy growths were all attacked and eaten by their fellow Pheru, which in turn suffered (widespread) abortions and genetic deformities. Meanwhile the human and San'Shyuum researcher where searching for a cure, not linking the powder and the deformities. As no cure was found, researchers concluded that the deformities were due to overbreeding. All human and San'Shyuum agreed to euthanize the Pheru, to their great dismay.
However, not all humans that kept Pheru did this as pets. Some humans (and presumably San'Shyuum) ate the Pheru, something that was not hindered by their genetic deformities. This caused the humans that ate the flesh of deformed Pheru to exhibit the same fleshy growths and behaviour that the Pheru did. This was the beginning of the Flood outbreak. This outbreak would continue as the Flood spores took more victims, until the Flood was recognised for what it was.
Taking up arms against the Flood, the Human-Flood war had begun. As the Flood became more intelligent due to technology consumption, the humans became more desperate for a cure of the Flood disease. The Flood would infect entire planets, and expand aggressively. Humans began to take over other worlds, to replace those who were lost. The inhabitants of these worlds would be annihilated and replaced by a human colony. It did not take long for the Forerunners took note of this, cursing the humans for their 'irrational violence' and 'aggressive expansion'. Humans had taken and colonised 50 defenceless Forerunner planets, and destroyed others infested with Flood with orbital bombardment.
The Human-Forerunner war was brutal, with the humans terribly outnumbered, but humanity still fought. The Forerunner military was led by the Ur-Didact, and the human-San'Shyuum alliance was led by Forthencho, Yprin Yprikushma and the First Prophet. Both armies fought each other at the start, while the alliance also fought the Flood concurrently. One of the very first major victories for the Forerunners was the capturing of Erde-Tyrene, a massive blow to the human's morale. Forerunners would use their advanced slipstream drives to skip unimportant worlds and instead target those strategically significant to the human-San'Shyuum alliance.
Meanwhile, the scientist Yprin Yprikushma had discovered something else. On a desolate planet at the edge of the galaxy, she had discovered an ancient being. The called it The Primordial, who hibernated inside a Stasis capsule of Precursor origin. She had brought this creature to a vast area on Charum Hakkor, still in stasis, and further securing it inside a Timelock, locking it in place and time.
Despite the advanced technology that held the Primordial in place, Yprin's research team were able to find a way to communicate. These were only for brief periods of time, and the prisoner's answers were mostly confused or unintelligible. Those in the know about The Primordial began to see it as an oracle and asked it questions to gain a greater understanding.
Here the humans learned about the human's true origin, but these disconcerting truths caused the human morale to crumble and thus contributed to the ultimate defeat of the human-San'Shyuum alliance. When they finally asked about the nature of the Flood, the answer horrified the humans so deeply, that many of them committed suicide.
While the Forerunner military alone would not be enough to defeat the alliance, the fact that they had to battle the Forerunners and the Flood simultaneously would be their downfall. During the war, the San'Shyuum would fight valiantly alongside their brethren, but they also suffered heavy losses. Before the final battle of the war began, the alliance's weaponry greatly improved due to advances made by humanity's Political and More commander Yprin Yprikushma, who used Forerunner technology to advance their own. This put humanity at Technology Tier 1, on equal footing as the Forerunners. Meanwhile, the Forerunner Builder caste engineered new weapons and vessels of their own, increasing their wealth and power immensely.
The human-Forerunner war had lasted to close to a millennium, and the human-San'Shyuum alliance had been pushed back to the Charum Hakkor system. The final battle would take place here, this final battle would decide the fate of the galaxy.
The battle was a harsh and bloody one, humanity, outnumbered and outgunned, were still able to hold the Forerunner army at bay. They used their ships to sweep across their controlled space to pick apart any ships that wanted to get into orbit. Had the ships made their intended vector, the humans knew that they would stand no chance. The final blow came as the Ur-Didact sent seven slipspace portals around the planet, and sent his entire military through, commanded by the Ur-Didact himself and his most experienced commanders. The Ur-Didact knew that he had sacrificed a great many ships, but also knew that overwhelming the humans was the only way to end the war. The human's last stand would be near the Primordial's cage on the planet's surface. A special force team of 7000 warriors and 70 ships led by Yprin were assigned to protect the Primordial.
The campaign lasted for 53 years, and caused innumerable casualties, among them the human commanders Yprin and Forthencho, and all of the Ur-Didact's children. The San'Shyuum leader would return to his homeworld, who promised to the Ur-Didact that he would reveal all of the Flood's secrets if they would return. Human researchers had used their last moments to destroy all their research data and physical evidence concerning the Flood, including their supposed cure. It was theorised by Bornstellar that this was humanity's last act of revenge, knowing that the Forerunners now had to face the Flood.
Humanity was devolved, all live humans were forced to consciously experience an artificially induced reversion of their evolutionary process, to the point of their bodies transforming to their ancestral forms and eventually losing intelligence. All members of the homo species were exiled to Earth, where the Librarian kept watch over them. Here they would stay, all but one members of the homo species would die out. Somewhere during the Human-Covenant war, humanity once again reach Technology Tier 2.