This has been hinted at by others, but this theory by Sauth pulls it all together.
This theory concerns Ghosts of Onyx
Sauth (sauthocles@gmail.com) writes:
The thing which most struck me about Ghosts of Onyx was the idea of ramping quality down, but production up, on Spartans. The idea of large-scale ground engagements in the Halo universe really grabs me.
It got me started thinking, though, on the particular shortcuts and changes in the S-III program. We're trading strategic thinking for easy mass-production, extreme aggression, and the ability to ignore damage that should be incapacitating. To counteract, we need a more clear-minded leader to keep the grunts in line.
Follow the movement in that direction as far as you can, and what do you get?
The Flood - and a Gravemind.
Spartan IIIs, a logical human reaction to a terrible opponent (the Covenant) and a faltering war effort, are almost like a mix between the Spartan IIs and the Flood. Given other examples of mass-produced, modular Forerunner tech (sentinels of Onyx), doesn't it seem interesting that the Flood are mass-produced and modular?
And doesn't it seem interesting that the human line of reasoning is leaning towards a mass-produced and modular solution? Seems to indicate that the Forerunner could have indeed been humans, and the Flood their army against some foe... until the Flood escaped their
control.