110,000+ years ago, humanity and Forerunners both possessed powerful empires in the galaxy. At the 110,000 BCE mark, humanity discovered abandoned ships with containers filled with a strange powder substance. The substance was tested and found to be an inert organic molecule of some kind, nobody knew exactly what.
Some people tried to use this powder on a domesticated animal called the Pheru, which were largely popular in human and San 'Shyuum households. Over a number of generations the Pheru treated with this powder began to develop mutations like multicolored soft fur, which were thoughts to be a rare and welcome change. These mutations eventually manifested in odd growths. Some Pheru started to cannibalize their kind and began killing and eating the mutated Pheru.
At this time humanity realized that these mutations may be a threat, so they disposed of their pets. It was, however, too late. Many humans had become infected with this powder, along with some San 'Shyuum. The powder began to manifest growths and caused cannibalism among the people. Thus, the Flood was born.
The infected humans began to infect others extremely quickly. Very soon, what was now the Flood had begun to spread outward and infect as many worlds as possible.
In response, wherever the Flood went, humanity attempted to sterilize it by burning planets. In some instances, Forerunner worlds would become infected, and in response, humans would sterilize their planets, killing an untold number of Forerunners.
Naturally, the Forerunners took offense to this. The Forerunners had always seen humanity as too aggressive and thought we were killing Forerunners to expand the human empire. Thus the Human-Forerunner war was started.
For around 1,000 years the Forerunners battled the humans while the humans battled both Forerunners and the Flood. However, the Forerunners were unaware of humanity's struggle on 2 fronts.
In an act of extreme desperation, humanity attempted to halt the Flood by infecting fully 1/3 of their entire population with a Flood killing antidote and sacrificed them by placing them in the way of the oncoming Flood. This antidote and sacrifice was enough to kill off the majority of the Flood, with the small amount left abandoning the galaxy.
With their numbers low, the Forerunners eventually fought the humans world by world until they staged their last stand at the planet Charum Hakkor, which used to be a Precursor hub world and was densely populated by humans.
For 50 years Forerunners attacked humanity without relenting until finally, they broke through and destroyed humanity's last defenses. After defeating humanity, the Forerunner learned that humans had been fighting a war on 2 fronts. They discovered how dangerous the Flood was, and never wanted to fight against it themselves.
The problem was, Forerunners did not know how humanity had stopped the Flood. So, in the event that the Flood ever returned, the Forerunner wanted to keep some humans alive for their memory and knowledge instead of completely eradicating our species.
Using the Composer, the Librarian and Didact composed a large number of humans and implanted all their memories in another group of humans. Any humans that were allowed to live were devolved back to a primitive stage and were placed on a planet called Erde-Tyrene (or Earth) under the care of the Librarian.
9,000 years later, the Flood came back with a vengeance. And thus began the Forerunner-Flood war.