Okay, I've been giving it thought and I'm sure that something similar has been posted on the topic (if not here than on the Halo Story Page). DISCLAIMER: I have very little evidence to support this theory, it was mostly thought up because of several quotes from Joe Staten:
HSP: The Flood are more than just a biological curiosity to the Forerunner.
JS: Curiosity? No. The Flood was the Forerunner's undoing - an overwhelming antagonist they could not defeat without putting a gun between their collective teeth, and pulling the trigger.
HSP: The Covenant released the Flood.
JS: No rational beings would ever knowingly release the Flood. Or, if they did, one would hope they had a damn good reason.
I believe that the Flood is a creation by the Forerunners. What initially led me to that conclusion was Joe's choice of words, specifically "The Flood was the Forerunner's undoing..." "Undoing?" sounds like they brought the Flood upon themselves, which leads into my theory.
The Forerunners being such an advanced race had grown large and powerful. Perhaps, they were powerful enough to think themselves gods, after all they first gave machines life, as evidence by the eons old Sentinels and Monitors. Perhaps, the even tried to modify their genes, and made themselves perfect. Perfect, except that the were still mortal, still chained to their existence until it ended. Hence, their "damn good reason." They decided to either create or modify a symbotic organism, so that their relationship with it could pronlong their life. But you know what they say about the best laid plans.
Perhaps, at first the Forerunners willingly submitted themselves to the symbiote, unaware of any danger. But the symbiote also took gained from the relationship, the knowledge of the original being, and it found it wanted more. Perhaps, the symbiote realized that it could control the host, in minute ways first, then it began to escalate until it controlled the host entirely. That's about where it mutated, or evolved. It began to consume the Forerunners, and their knowledge, and anything and everything in its path, hence the the name Flood.
Like Icarus, the Forerunners fell and they tried desparately to take the symbiote now parasite with them. At the beginning of the level with the same title, Gravemind tells us, "[he is] a monument, to all [our] sins." What "sins"? The sin of trying to be god(s)? The blood on the hands of the decedents of the Forerunners (us)? Hmm, I seem to have drifted off-topic, but I think that about wraps it up. Someone want to get the flak guns ready and fill this full of holes?