106,538 BCE
From Halopedia, the Halo wiki
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c. 109,040 BCE, human colonists arriving at a ravaged planet on the edge of the Milky Way Galaxy discover an exceedingly ancient stasis capsule. This capsule is the prison of the ancient Precursor and Gravemind known as The Timeless One. Yprin Yprikushma transports the capsule and its prisoner to Charum Hakkor for further study.[1]
Eventually, humanity discovers a way to fight the Flood and contains the infection while it is still relatively minor, removing all traces of its existence within the Milky Way. Throughout the war, most Forerunners remain unaware of the Flood's existence, believing stories of the parasite to be an excuse for humanity's aggressive expansion. The Flood will not seen again for nine millenia.[2]