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Likely. You've heard about the discovery of the Spirit of Fire's wreckage, right? How the flood hijacked it from shield world 0459? It's heading towards UNSC controlled space currently on the halo timeline.
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In the comic not sure which one set after halo 4 they showed a flood parasite on the I think the forward onto dawn. So they may have a come back in halo 5
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I don't know if they ever come back, (i haven't been up to date in the Haloverse) but it will be cool to see prometheans vs. Flood.