From Halopedia, the Halo wiki
The Great Purification was the culminating act of the Forerunner-Flood war in 97,445 BCE, when the seven rings of the Halo Array were fired. The rings' combined pulses scoured the entire Milky Way galaxy, disabling the Flood and wiping out all sentient life that was not safely outside its range at the Ark. The effects of the firing had lasting effects on the galaxy for the next 100 millennia, marking the end of the Forerunner ecumene and eventually leading to the rise of the Covenant and humanity.
After the Flood appeared defeated by early humanity, the Builders, led by Faber-of-Will-and-Might insisted that stronger measures needed to be put in place across the galaxy in case the Flood should ever return. They proposed the assembling of the Halo Array, enormous ringworlds that fire a wave with interstellar range that would purge the galaxy of Flood infection by killing all carbon and calcium-based lifeforms on which it fed. While this proposal was met with immediate outrage from the Didact and the Warrior-Servants, the Librarian and her Lifeworkers reneged to the plan if environmental steps were taken to preserve as much of the galaxy's wildlife and races as possible for reseeding after the Array was fired. These two suggestions were approved and the Halo Array was assembled, designed as both a weapon of mass destruction and nature preserve.
The Flood eventually returned to the galaxy, but as the war escalated and the parasite spread even further, the Didact (now two individuals) remained steadfastly opposed to firing the rings. Both of them viewed galactic genocide as a violation of the Mantle, the Forerunner code of doctrine. While the IsoDidact refused to fire on moral grounds, not wanting to kill billions of innocents, the Ur-Didact rejected the Halos on societal grounds, certain that the Great Purification would cause the end of Forerunner dominance over the galaxy. Both of them delayed activating the rings by attempting alternate plans to defeat the Flood, including the anti-Flood AI Mendicant Bias (who went rogue and defected to the Flood) and the creation of mechanical Promethean Knights, which were created from unwillingly transformed humans, thereby causing genocide to prevent genocide. Neither of these measures succeeded in defeating the parasite.
By 97,445 BCE, the Forerunners were badly losing, most of their population had been lost, and the Flood had reached almost complete control of the galaxy. With much reluctance, the IsoDidact fired the Array, initiating the Great Purification. The blast resulted in the death of the Flood and everyone else in the galaxy, including the Librarian herself.
The Great Purification was not the first time a Halo had been fired. A ring of the original array had been fired by the Master Builder at the Charum Hakkor system to test its effect on the native wildlife. Later a pulse was fired on Janjur Qom to punish the San'Shyuum there who rebelled against the Forerunners. At the Fate of Maethrillian Mendicant Bias took control of five of the nearby rings (which had been assembled for decommissioning) and attempted to fire all of them; at least Installation 07 was successfully fired while the Forerunner defense fleet managed to destroy at least one of the rings. The last use before the combined wave from the Array was at the Battle of the greater Ark, when Omega Halo was fired, damaging a formation of Precursor star roads and wiping out all life in the Large Magellanic Cloud. None of the Halos were used again until 2552, but each had their firing halted or contained to prevent such widespread devastation again.
The Great Purification marked the end of the Forerunner-Flood war. Just before the firing, the galaxy had been teeming with Flood, who had progressed to an interstellar threat, consuming whole star systems, forming advanced Flood intelligences called Key Minds, and able to interact with the fabric of the universe itself, halting slipspace travel across the galaxy. Immediately after the firing, the Flood was neutralized. Flood and sentient lifeforms on planets that had been seeded with solute beforehand were disintegrated. Forms in starships and non-soluted sites were killed but not melted, their bodies remaining but their nervous systems irreparably destroyed. The remaining Flood spores and combat forms that were left were taken to the Halos and other sites for study, in hopes that a cure could be found should the Flood ever return.
The ongoing space battle of the Forerunners and the Flood, the Battle of the Maginot Sphere, had its order completely reversed. Mendicant Bias' Flood-controlled fleet had been fighting with Offensive's Forerunner-and-mechanical fleet, but within moments the rogue AI suddenly found itself with ships without any living crew. Offensive used Mendicant's momentary confusion to gain the upper hand, commanding his remaining ships directly and destroying the majority of the Flood's fleet in under 90 seconds. Mendicant was subsequently captured and imprisoned at Installation 00.
The combined massacre of the rings and of the Battle of the greater Ark reduced the Forerunner population to less than a fraction of what it had once been. There was no hope of rebuilding their lost empire, and the survivors felt guilt over their imperialism in the name of the Mantle, which had let the Flood conquer as far as it had. Led by the IsoDidact, the last Forerunners left the Milky Way to build a new home elsewhere, commissioning humanity to one day take their place. All species brought to the remaining Ark were reintroduced to their homeworlds at a pre-Industrial Tier 7 level, and roughly 90 millennia passed before any of them became space-faring again.
The biological effects of the rings had long-term consequences on the galaxy's ecosystems. Because the Librarian could not rescue every species, all of the specimens left behind were wiped out and rendered their species extinct. Those species that had been saved on the Ark were reseeded afterward, but the gaps in the food chain were significant enough that during the dark time many more species went extinct due to their permanently altered environment. While the Conservation Measure did its best to eliminate any trace of genetic disruption, scars still remained in the fossil record. In 2332, human scientists discovered a curious anomaly dated to Late Pleistocene, in which no fossils dating to roughly 97,000 BCE were discovered on worlds colonized by humans. The Ross-Ziegler Blip, as it was called, was initially dismissed as a random aberration caused by spatial distortion, out of doubt that an interstellar extinction event could have occurred simultaneously on every planet. After the Halos were discovered by humanity, the Blip was reinvestigated, its cause now identified as the disintegration of most biomass in the galaxy during the Great Purification.
An unexpected effect of the Halos' firing was that Precursor artifacts were destroyed as well. This was due to the Halos interacting with neural physics, which held Precursor constructs together and made them nearly unbreakable. Firing a Halo in the vicinity of the artifacts would disrupt the exotic neurophysical binds and thus disintegrate the relics. While initially viewed as an unfortunate side effect, as when Installation 07 was tested at Charum Hakkor, this disruption turned into a small advantage for the Forerunners in their war against the Flood, letting them use the Halos to destroy Precursor star roads that were being controlled by the parasite. When the Great Purification occurred, every Precursor artifact in the Milky Way was destroyed, leaving no trace of them for modern civilizations. Shortly before the blast, the Gravemind revealed that the Domain, an immaterial dimension used by the Forerunners as a repository of knowledge, itself was a Precursor creation and so would be wiped out with the Flood. As such, when the rings fired the blast erased 100 billion years worth of stored knowledge and recorded history.
When the reseeded civilizations of the galaxy rebuilt in the following millennia, they were left with only distant historical fragments of the age of Forerunners. The San'Shyuum, initially rebellious against the Forerunners, turned to worshipping their long departed oppressors. Without the complete account of what had happened, the San'Shyuum came to believe that the Halos were great machines designed to ascend its users to godhood. Their interpretation of the fragmentary texts was that the rings summoned sublime energies that burnt away falsehood and freed the soul from the material world. The Forerunners, according to them, had become spirit and reigned as gods, and had left their relics and holy texts behind to inform the other races on how to ascend like them. This legend about the Halos came to form the basis of the Covenant religion, and the Covenant was formed as an interspecies union that together would seek the sacred rings.
There were some doubts among the Covenant that the legend was true. Some Sangheili, such as the clan of Ussa 'Xellus, believed that the rings did not exist but were a lie made up by the San'Shyuum in order to deceive species they enslaved. One of the San'Shyuum Prophets, Mken 'Scre'ah'ben, had doubts about the rings' function, since to him the descriptions of the Halo effect sounded close to that of weapons. Another San'Shyuum, the future Prophet of Truth believed in the rings and initiated their firing, but feared that some of the faithful could be left behind and not ascend, after discovering that humans were, by his interpretation, un-ascended Forerunners. Truth thus resolved to eliminate all opportunity of doubt for the Covenant, demanding the extinction of humans before their status was discovered then ordering the Sangheili assassinated and replaced with Jiralhanae when many Elites began to question the claims of the Prophets.
The truth of the Halos of what happened to the Forerunners was revealed in 2552, when 343 Guilty Spark, the Monitor of Alpha Halo explained their true use to the Covenant and humanity. Some, such as the Brutes and the Prophets chose to reject his words, and so nearly initiated a second Purification twice, at Delta Halo and then at the Ark. Others, like humans and the Sangheili, accepted his words and put their efforts into preventing the firing of the rings. While humanity willingly fired a single ring, Installation 08, at the very end of the Human-Covenant War, the ring was safely kept out of range from the rest of the galaxy so its effects would be confined to the Ark.
A few Forerunner survivors emerged in the years after the Covenant War, resentful of the Purification's destruction of Forerunner civilization. After an initial attack on Earth with the Composer failed, the revived Ur-Didact attempted revenge on humanity with a captured Halo ring, abandoning his principles to never use them. Another ancient, 000 Tragic Solitude, once the Forerunner politician Splendid-Dust-of-Ancient-Suns, used the threat of a second Purification to trick humans into opening a portal from Earth to the Ark, feeling that the species of the galaxy deserved to be wiped out for their own mistreatment of the Array. To prevent further incidents, standard operating procedure when encountering a new Halo was to secure its control room and activation index so that the ring would be prevented from firing.
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