All you have to do is make explosives sensitive to rapid cell recomposition and install it into every Forerunner and Ancient Human. The logistics aren't too out there. And not much the Flood can do about it, being that any infected individual gets blown up and has their brain destroyed.
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This is simply a more elaborate Halo Array. The logistics of installing such a device is crazy.
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Elaborate? It's a bit of explosives put in every person. Didn't they already undergo surgery to make themselves better? And the Halo Arrays have better logistics? "We have a plan that will stop the Flood. Blow up anything that gets converted using special bombs, perhaps in the form of bacteria or whatever." "No, that's a crazy idea. It'll never work! We're going to use several massive rings to send out a pulse that will destroy all sentient life in the galaxy. See, now that's a plan!"
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The huge glaring flaw that you're missing is that you'd need to install the explosive into nearly every form of life. That goes for trees and large plant mass too.
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Oh, simple enough. Make an all-consuming life form that explodes, or at least spontaneously combusts, when it becomes infected with the Flood Super Cell. Best plan ever. [spoiler]In case you haven't noticed yet, this is a joke.[/spoiler]
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After a certain point, Flood infection stops being about controlling a host and just absorbing more biomass. All this does is cut their food down into more edible chunks.
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It doesn't kill the spores though. Killing the hosts accomplishes nothing more than the Halo array did.