When the Flood began its campaign of infection in the Milky Way galaxy, the Forerunners found themselves woefully unprepared to fight an enemy of any sort on such a massive scale. Much of the early decades were spent simply trying to understand what they were fighting - the idea of a purely biological foe that could oppose the Forerunners themselves, the supreme masters of technological superiority, was utterly alien to them. So many colonies fell as the Forerunners hesitated, but that does not mean they were totally inactive.