Looks to me like you need to learn a bit more about the history of the Flood. I will give you a shortened version. The Ancient Humans and Prophets (the ones that lived before the Halo rings were fired) first found the Flood in a dust form floating in containers in space. They learned that when fed to Pheru, a popular species of pet, that they would produce desirable traits. They fed the powder to Pheru for many years, but strange things began to happen. Powdered Pheru began to have strange growths and these growths, and sometimes the entire Pheru, would be consumed by other powdered Pheru. (Pheru are naturally herbivores.) Eventually the Flood evolved into the form that we fight in Halo and fought a war against the Ancient Humans and Prophets. The Ancient Humans and Prophets discovered a way to beat the Flood. they manipulated key strands of Flood DNA, infected a third of the population, and placed them in the path of the Flood. This reprogrammed the intentions of the Flood, causing it to turn on itself. The stable Flood that remained knew that they faced their ow extinction and fled the galaxy. The Flood returned 10,000 years later and began it's conquest of the galaxy, starting the war with the Forerunners.