Based on some of the level names and other bits of info released before Halo 3 was out I speculated that The Chief would activate the remaining Halos in order to destroy The Flood, sacrificing himself while a large portion of Humanity escaped the effects by traveling to the coverage gap left by the destruction of Halo 04.
I guess Bungie did the inverse one me, moving the Flood to a place where a Halo could fire without effecting any of our galaxy.
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