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Extinction is a term regarding the disappearance, or dying out, of an entire species. Extinctions are a natural phenomenon that have occurred throughout the history of many worlds, often brought on by cataclysmic events. The greatest mass extinction in the Milky Way galaxy resulted from the Great Purification at the end of the Forerunner-Flood war, in which the activation of the Halo Array wiped out all sentient life within three radii of the galactic center. Various plants and animals have also gone extinct as a result of being unable to adapt to changing environments on their home planets. During the dark times, a number of species that were reintroduced into their homeworlds by the Forerunners became extinct. Many other belligerent species in the Orion Arm region have been brought close to the brink of extinction as a result of War, oftentimes when their civilizations enter an atomic age and employ the use of nuclear weaponry.
Extinct alien civilizations
- Around 10,000,000 BCE, the advanced Precursor race were driven to near extinction by their creations, the Forerunners. In the face of extinction, most of the Precursors reduce themselves to inert powder, intending to regenerate their forms later. However, this dust would deteriorate over eons, eventually bringing forth the parasitic Flood. Circa 106,538 BCE, a mysterious being known as the Primordial was discovered in stasis capsule by ancient humanity. When found by the forerunner Didact, the Primordial claimed to be the very last surviving Precursor. Prior to being disintegrated by the IsoDidact in 97,445 BCE, the Primordial revealed that more Precursors may have survived their war with the Forerunners.
- The Forerunner race reigned for millennia as the ascendant civilization in the galaxy until the activation of the Halo Array, their Pyrrhic solution to halt the Flood, in 97,445 BCE. Although they themselves are essentially extinct, evidence of their existence remained, spread across the galaxy in the form of numerous creations, installations and artifacts.
- In 97,445 BCE, monitor 343 Guilty Spark learned a young alien civilization existed within a great dense cloud, possibly a star nursery. This alien race had gone unnoticed and unindexed by the Flood and the Forerunners at the time of the firing of the Halo Array. Having not been included in the Lifeworker's Conservation Measure, the species became permanently extinct when the Halo pulse killed all life in the galaxy. Nothing was known about them or their history, other than that their first and very last signals to the stars were calls for attention.
- Many centuries prior to the twenty-sixth century, a civilization existed on the planet Netherop in the Ephyra system. It ultimately died off before achieving spaceflight due to excessive heat created by greenhouse gasses.
- Prior to 860 BCE, an unknown bipedal species that inhabited the Planet of Blue and Red had gone extinct. This alien civilization had left behind carvings in their stone cities which exhibited their knowledge of the Forerunners. Because their planet harbored ancient Forerunner technology, both the San'Shyuum and Sangheili race saw their ruined world as a strategic location during the War of Beginnings.
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Near-extinctions (Endangered species)
- When the Great Purification occurred, ending the Forerunner-Flood war, a small minority of Forerunners fled the Milky Way Galaxy leaving their species nearly extinct at the time. The vast majority of their species died when the Halo Array fired as planned.
- By 850 BCE, thremaleon, a species of lizard from the Sangheili homeworld Sanghelios, was nearly extinct.
- Prior to their incorporation into the Covenant, the Jiralhanae race was almost brought to extinction due to a decade-long civil war known as the First Immolation. The war between the Rh'tol and Vheiloth skeins had plunged their homeworld, Doisac, into a nuclear holocaust that drove the species back several hundred years in science and machinery.
- Between 2525 and 2552, the Covenant conducted a period of genocide against humanity due to the discovery that they were set to inherit the Forerunner's technology. Although their efforts resulted in the destruction of hundreds of colonies and billions of human lives, they would ultimately fail. By 2553 humanity had already begun a strong recovery and would emerge as a superpower in the known regions of the Orion Arm by 2557.
- The fall of the planet Reach in 2552 brought moa numbers to near-extinction levels. However, moa still survive on Reach in remote sectors of the planet that were not glassed by the Covenant. Additionally, the entrepreneur Wiljax Brantley had received a shipment of moa from Reach prior to the attack. His Have S'Moa restaurant and petting zoo on Gannick 22 is now home to the largest single population of remaining moa in the galaxy.
- After the Fall of High Charity, the San'Shyuum population became dangerously low. In fear of being hunted by vengeful Sangheili, the survivors had gone into hiding. They are now an endangered species.
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- Halo 3, Bestiarum
- Halo: Silentium, page 329
- Halo: Silent Storm, Chapter 1
- Troy Denning on Twitter 
- Halo: Broken Circle, Page 3
- Halo: Silentium, page 314
- Halo 2 "They and all additional sentient life in three radii of the galactic center, died, as planned.", 343 Guilty Spark
- Halo: Broken Circle, page 100
- Halo Waypoint: Jiralhanae
- Halo: Contact Harvest, Chapter Sixteen
- Halo 3
- Halo 4 - "For too many years, humanity was on the backfront, reacting to threats rather than preventing them. The rest of the galaxy was bigger than us, stronger than us. We were mice, hiding in the shadows, hoping the giants would not see us. No more. Humanity is no longer on the defence. We are the giants now.",
- Halo Waypoint: Canon Fodder: Have S'moa
- Halo: Evolutions, "The Return", page 328