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 simultaneously one of its primary causes. The war destroyed countless human-populated systems and cost more than a third of humanity's population and 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 Forerunners, as well. Unfortunately, the Flood had taken their toll and, in their defeat, sounded the death knell 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 aggressively expand. Humans, in desperation, began forcefully taking worlds from other species to make up for the ones they had lost, initiating the Human-Forerunner war. However, the primary mission of the fleets under the command of the Lord of Admirals, Forthencho, was to locate and exterminate any presence of the parasite. When Forerunner worlds became infected, they were immediately targeted for orbital bombardment. As the Forerunners apparently did not believe the Flood a credible threat to their ecumene, these actions only fueled their hatred towards humanity.

As a further desperate measure, humanity's leaders decided to take a third of their population and genetically altered them by inserting genes designed to fight Flood biomass. They then took this third of the human population and allowed the Flood to consume them. 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 ultimately lead to the downfall of early mankind. Responding to the threat of the Flood, Humanity sought to buy time by conquering new worlds and species to replace those lost. This desperate aggression, combined with humanity's policy of immediate sterilization of any worlds infected by the Flood led them into a separate war with the Forerunners. While human forces were capable of dealing with the Forerunners on equal footing, the total forces they could commit were never enough to ensure victory. However, whether through sacrifice, technology, or willful retreat on the part of the Flood, humanity was successful in managing the threat of the Flood for a time. When the Forerunners eventually proved victorious in their own conflict, they devolved humans reducing them to a Tier 7 species. The Didact blamed humanity for taking the Mantle of Responsibility upon themselves, believing it was their reckless actions that brought the sickness into the galaxy. In truth, the Forerunners had even less success in battling the Flood than their human rivals. The Mantle, holding that all life was sacred, hamstrung Forerunner attempts to combat the infection, allowing the parasite to exponentially expand until no force could stop it.

List of appearances

 * Halo: Cryptum
 * Halo 4
 * Terminals