I actually don't remember the Flood reveal. I must have played it with my brother since we co-op'd the original two games. Unless you're totally oblivious to the series though it's one of those paradigm shift moments you don't see coming that are harder to do these days in gaming.
I do remember finishing up "Regret" with my brother, and then having to set the table. When we came back, the Gravemind cutscene was going, and we were confused how the hell we were talking to this plant thing. The cut Halo 2 mission with the Gravemind's tentacles slithering around in the background, etc., would have made that reveal work so much better. Le sigh.