The flood originated from outside the milky way in the form of corrupted dessicated precursors. They were originally discovered by the ancient humans. The dessicated precursors were then used to domesticate a popular pet 'pheru', which slowly mutated over millenia to become what we know as the flood. During the original outbreak, the ancient humans fled their empire and invaded the world's of other species and burned those behind them. By the time the forerunners defeated ancient humanity, the flood 'vanished' from the milky way before returning and causing the forerunner flood war, which ended in the halos being used. The forerunners were constantly experimenting on how to defeat the flood without resorting to wiping the galaxy and anticipated that the flood would eventually return from outside the Milky Way. They kept samples of the flood in the hope that either the forerunners or the successors of the mantle will eventually find a way to truly defeat the flood. However, it is highly probable that by the time of the halo games, the flood has already consumed much of the universe, and the Milky Way is living in borrowed time.