Well, the darkness that caused the downfall of humanity was technically the "Ahamkara" which are dragons in the destiny universe. The Flood vs Ahamkara I think Ahamkara would win personally. With Atheon its a bit more complicated, He could send the flood into the past or future with a slipstream.... over and over again. With Crota i think the only difficult part for the flood might be Crota himself, If a single flood dies the oversoul kills everything..... and if the flood continued to fight they would die out.