Well I'm not LoA so I might be wrong,and since you're playing [b]through[/b] it,I'll leave it in spoilers. [spoiler]the flood isn't completely gone,most of them are.During the fight on the ark,the flood crashed into the ark on High Charity.This was to stop the activation of the halo rings.But cortana had a way to cause a localized blast,meaning the firing radius will only be as big as the ark I believe.When the UNSC and covenant separatists escaped after activating this blast,the flood was left on the ark.The blast killed all flood present on the ark and severely damages the installation.Even so,the flood isn't completely gone.[/spoiler]