It would not be the Covenant because it fractured at the end of Halo 3, or the flood because the firing of the unfinished Installation 4 (b) destroyed the Gravemind. It could possibly be Sentinels or some other Forerunner technology, or even an as-yet unseen enemy.I don't know this is a very good question though. I can't wait to find out.
^It could be the flood, they just destroyed THAT gravemind. There are other Halos and that means more flood... just thought i'd point that out.
^I fully agree with you! I mean, who was that voice in your head giving you more trauma in the Halo 3 level "Halo" when you entered the Control Room? Another Gravemind. So, that means the one that's been trying to kill you throughout Halo 2 and Halo 3 is destroyed. Or, maybe (possibly) he's still alive (No pun intended). And yes, very good question indeed, tip top guy.
i think its the forerunners and the precursors (if they're alive) are your allies
It is the Promethians, a race that was left behind on the shield world Requiem. They are kind of the protecters of that world. Requiem was a world that was untouched by the flood, and therefore was made a shield world by the forerunners for the species there.