We ain't seen nothing yet? The Flood may have more secrets than we imagine (as if there weren't enough already):
bhoo (firstname.lastname@example.org) writes:
Very few people (as far as I can tell) have wondered what the Flood are going to evolve into by the end of their parasitic metamorphosis. What if 343GS destroys their food so as to not let them get that far? What if the flood ARE the Forerunner and that 343GS killed them off long ago for some devious reason and cannot allow them to "re-evolve" and get their revenge on him (assuming that the spores still contain memories from the past fight with 343GS)?
And maybe 343GS had kept some Flood alive in order to attempt to retrieve some memories or info from whatever "brain" they may have in spore form (those computers are all about retrieving as much info as they can, regardless of the dangers that may present).
But now that Master Chief destroyed Halo 004 (and any chance of retrieving memories from the flood spore), 343GS may have added him and the rest of Humanity to his list of enemies to destroy. If this AI is as vengeful and mean-spirited as I imagine him to be, then I wouldn't put it past him to align himself with the Covenant in some way, shape or form to take down Earth for good.