Human-Flood war

The human-Flood war was a major conflict fought between ancient humans and the newly arrived Flood. It took place concurrently with the Human-Forerunner wars, and was simultaniously one of its primary causes. The war destroyed countless human-populated systems and cost more than a third of humanity's population & resources. Despite the setback of two massive wars ongoing at the same time, Humanity managed to prevail over the Flood and still nearly prevailed over the Forerunner, as well. Unfortunately, the Flood had taken their toll and, in their defeat, sounded the deathknell of early human civilization.

First Flood contact
During their colonization of other planets, humans discovered automated cargo ships of unknown origin, which had supposedly arrived from one of the Magellanic Clouds, crashed on planets near the edge of the galaxy. The humans found no crew, with the ships appearing to be automated, but they did find millions of small transparent cylinders filled with an unknown powder. Initial testing was done in the strictest containment. These early tests showed the powder to be harmless and useless, being composed of lifeless short-chain organic molecules. Early experiments demonstrated psychotropic effects on some smaller domesticated animals, one of which being the Pheru. The powder tests on the Pheru proved to be initially harmless, and indeed appeared to encourage desirable traits to appear in their appearance and behavior. However, the powder was in fact composed of Flood genetic material, and over time it began merging with and altering the genome of the Pheru in order to generate its own Flood Super Cells. Over time, the infected Pheru began to infect others and even began showing some symptoms of the Flood mutation, such as fleshy tentacle-like rods. Close contact with the Pheru spread the infection to humanity. Some San 'Shyuum were also infected as the Pheru were also kept as pets on the San 'Shyuum worlds. Eventually the Flood began to spread, and the Feral Phase was initiated. At this point, human researchers attempted to ask the Timeless One about the Flood. They received answers so traumatizing many of them committed suicide rather than live with the knowledge.

War
By the time the human officials discovered what the powder had done, it was too late. Entire planets were infected, and the Flood began to ravage worlds and systems. This also initiated the Human-Forerunner war, because humans, in desperation, began forcefully taking worlds from other species to make up for the ones they lost to the Flood. When the humans attempted to quarantine the worlds, more infected escaped, and thus a drastic measure was invented. Despite how sacrificial it was, it worked.

The human leaders decided to take a third of the population and genetically alter them by inserting genes designed to fight Flood biomass and destroy the Flood gene imprints. They then took this third of the human population and "fed" them to the Flood. The new genes aggressively killed off Flood biomatter and destroyed the Flood until the few that survived were forced to escape. They would not reappear for another 9,000 years.

Aftermath
The human-Flood war ravaged humanity and forced them into a war. Humanity began irrationally conquering new worlds and species, taking new planets to replace their own. This caused the Forerunners to act according to their Mantle, and declared war on humanity. This also weakened humanity's war front, as they were forced to fight the Flood and the Forerunners at the same time. With the Flood ravaging human worlds on one side and the Forerunners pressing closer on the other, humanity was doomed. Eventually when the Forerunners won, they devolved humans, reducing them to a Tier 7 species.

List of appearances

 * Halo: Cryptum