They were originally wiped out in the Human-
Earth (known as Erde-Tyrene by prehistoric humans and Forerunners) is the third planet of the Sol system, and one of its four terrestrial worlds. Homeworld of the human species, Earth has been at the forefront of galactic history, from encounters with the Precursors to the end of the Covenant Empire.
March 3, 2553, saw the end of the Human-Covenant war as a Pyrrhic victory for humanity and their new found Sangheili allies - the majority of the Covenant Loyalist military having been defeated at Delta Halo by the Sangheilian Fleet, and the rest annihilated by the joint Elite-UNSC forces at the Ark.
As punishment for defying the Forerunners, nearly all of humanity was wiped out and the remnants and technological achievements of their civilization were extirpated.
Spoiler warning for Halo: Infinite. Yes it was completely destroyed.
By the 26th century, humanity, led by the United Nations Space Command (UNSC), is caught in a war with an alien coalition known as the Covenant. The Covenant worship the Forerunners as deities, mistakenly believing that the Halos are a tool of salvation, not destruction.
As far as I know wiki says that Before, during and after the war Elites respect humans. Even they are enemy to them, they respect them with greather honor. They consider them as brave, honorable and even stronger to their own race.
Endangered Species: Humans Might Have Faced Extinction 1 Million Years Ago. New genetic findings suggest that early humans living about one million years ago were extremely close to extinction.
According to Halo lore, the Flood is a product of a war between the Forerunners and the Precursors. Some Precursors, who lost the war, were turned into regenerative dust that created horrific mutations. The remaining Precursors assimilated into this newfound corruption.
The Human race was origanally based on Erde Tyrene (Earth) and became a tier one civilization (the peak of technological advancement) with their capital planet being Charum Hakkor.
Modern humans originated in Africa within the past 200,000 years and evolved from their most likely recent common ancestor, Homo erectus, which means 'upright man' in Latin. Homo erectus is an extinct species of human that lived between 1.9 million and 135,000 years ago.
Mid-26th century depictions of North America seen in Halo 2 and Halo 4 prove that the continent still holds a similar shape to its 21st century appearance, with Hudson Bay, Quebec, and northeastern Mexico still intact.
Installation 04, also known as Alpha Halo, or simply Halo, was one of seven ring-shaped superweapons that comprised the Forerunners' Halo Array. It was located in the Soell system in the Orion Arm and was the closest Halo ring to the human sphere.
Britain, seen in the center left with the lights of various cities shining at night. Britain is a region of formerly constituent parts of a defunct nation.
76 Spartans were killed at Laconia Station by Cortana in Halo 5. Overall, there was an estimated number of 7150 troops on The Infinity. It seems like Pablo Schreiber – sorry the Master Chief – is the only survivor of the Spartans.
However, their infected hosts do. The Halo pulse wiped out all of the infected hosts, and all beings who could potentially become hosts, thus depriving the Flood of the ability to infect anything, rendering them inert. Eventually the Flood, without sufficient living biomass to sustain itself, died off.
The Endless survived the Halos firing, and were found afterwards when the preserved species on the Lesser Ark were returned to their homeworlds. The only canonical means for an organic creature to survive the Halos without being on the Halos themselves is to be in temporal stasis, like the Primordial was.
The humans though are always portrayed as the ultimate good guys trying to overcome the alien and evil Covenant in Xbox's flagship franchise. But don't be fooled by their struggles though, the humans have done plenty of bad, too.
In the Halo 4 terminals, Forthencho is shown eradicating a Flood presence on some planet prior to the human Forerunner war. In Cryptum, Forthencho is alive at the end of the war, which I believe lasted 1000 years.
The only way to stop the Flood is to starve them to death. Cortana to John-117 and 343 Guilty Spark. John-117 fends off the oncoming Flood Combat Forms and Infection Forms on Installation 04.
The Mgalekgolo, aptly named Hunters, are among the most formidable and distinguished species within the Covenant's roster and possibly the universe.
The weakest and most comedic of all Covenant enemies are the Grunts.