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.
English
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Sending the flood into the past or future doesn't suddenly mean the vex win, quite the opposite even. Flood in the past means more time to grow, while flood in the future means even if the vex somehow win which they wouldn't, they would have to again. The Ahamkara are biological meaning they would not win.