How did they contain the Flood so well in CE 2 and 3? I remember the flood could board ships and stuff how did they get them all into one place at one time to explode that halo and finish them off? Also, do you think Bungie handled the whole "Flood are super important while covenant are second" thing well because it seemed the same formula in each game, you are fighting covenant then suddenly "the flood are here to make everything gross! run!" and then you blow something up.
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You can't really kill the flood with military methods other wise the Forunner would have never went into exiction. You can only control and contain Flood out breaks by starving them. So if the Flood has no food they go dormant until more food arrives.