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Posted by: dahuterschuter
Because they're collectively controlled by the Gravemind or Babymind in CE's case. It doesn't care about losing a few combat forms, it does care about getting a ship online.
I havent read the books, but I personally think the old Gravemind on delta halo controlled the flood on installation 04 when they were released, then the gravemind coordinated the flood to infest T@R. Afterward, when the chief extracted the captains chip from the brain form, the gravemind seemingly sent wave after wave of flood to stop him after he escaped T@R. (I believe this theory, because the flood were really determined to stop him on the last level in halo CE)