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At the end of Halo 3, the biggest part of the Flood and the Gravemind were killed after the firing of Installation 4(b). However, since the Halos were built to not only eradicate the flood but also to study them, it's very likely that the other 5 installations still out there have Flood specimens on them. Also, there is no guarantee that all the Flood left Installation 05 when Gravemind left for High Charity.

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