I am a Halo Enthusiest that loves to talk about the universe. Though I may not be the best multiplayer, I play for the fun and the unforgettable moments. If you play for a good time and for a little competition, then im your guy.
After the events of Halo 3, the Covenant was broken to pieces due to the death of the Prophet of Truth and the destruction of the capital city High Charity by the flood. The KNOWN Flood contaminent on High Charity, The ark, and the new halo ring was subsequently destroyed by John 117 and the Arbiter. So if we use this information we can agree that the UNSC and the Sanghelli Seperatist allies were the victors at the time. Now about the Flood:
It is highly likely that the Flood was not completely destroyed after these events because there is still a high chance that there exists undiscovered Forerunner planets and installations in the universe. This being said it is possible that there are Flood contaminants active there.
That being said the Flood did not obviously win but they can still be considered a threat. This threat though is not as major as it was in the trilogy.