This article is going to be a bit different. Because so little is know about the Precursors and their connection to the Flood, this post will necessarily be based largely on my own speculation. The Precursors have only just begun to be explored, most notably in the recent forerunner trilogy of novels. Much of my information will come from the first two novels of that trilogy. Warning - because I rely on those two novels this post will include some spoilers and should be avoided if you have any desire to read them.
I’ve already mentioned the Precursors in the post about the Forerunner. While the Forerunner are idolized as Gods by the Covenant and their member species, it appears from the fiction to date that it is the Precursors who possess “God-like” powers – that is they appear capable of creating entire species. The precursors are believed to have created the forerunner and humanity and presumably all other species in the Galaxy. The Precursors were not of this Galaxy but they seem to have used it as a testing ground for the various species they created. Turns out, not many of the species passed the tests. For unknown reasons, the Precursors would eventually kill off the species they had created. As I said in the Forerunner post, the precursors developed a pattern in which they would introduce species into the Galaxy, nurture them, and then without explanation, eliminate them.
The Forerunners were scheduled to meet this fate as well. However, they fought back and eventually pushed the precursors out of the Galaxy. The Precursors seemingly disappeared, and after 100,000 years even the Forerunners had lost nearly all memory of the Precursors. But the Precursors were not done with the Forerunner. Instead they created another species and sent it to extract revenge against the Forerunners – that species was the Flood.
To talk about the Flood is to really talk about the Gravemind – which is the central intelligence of the Flood infection. In truth there is not one Gravemind; each outbreak of the Flood can create a Gravemind that is unique. The Gravemind is created when an individual Flood spore takes on multiple sentient beings. This is known as a proto-Gravemind. If not destroyed a proto-GM will devour more and more sentient beings and will eventually become self-aware. At that point it becomes a full Gravemind and can move independently and can direct the remaining Flood spores.
The First Gravemind was captured by the Forerunners shortly after Ancient-Human/Flood war. Because the Gravemind was sentient the Forerunners recognized its value as a source of information on how to combat the Flood. Forerunner also recognized the risk of allowing the Gravemind to live. They held it captive on a secluded and abandoned planet and began to interrogate the creature. It claimed to be the last Precursor. But other than that the creature spoke in riddles and gave the Forerunner's very little useful information. However, when alone with individual Forerunners the Gravemind would tell them the secret of the Flood. The knowledge was so devastating that when these individuals heard the secret they would immediately commit suicide. Some believed the creature was simply manipulating these unfortunate Forerunner and all interrogations were ordered to stop. Instead they ordered the AI Medicant-Bias continue the interrogation - thinking the AI would be safe from any manipulation. In fact, the AI was corrupted and was under the influence of the Gravemind when he took over the Halo array and tried to fire them within the Forerunners capital city.
The Gravemind remained captive for 10,000 years. When the Forerunners test fired the first Halo ring the shockwave destroyed the prison that was holding the Gravemind and he escaped. The Didact came out of his self-imposed exile to try and capture the Gravemind. When he eventually captured the the Gravemind he was told the secret of the Flood. The Creature informs the Didact that humanity did not defeat the Flood. The humans only survived the Flood infection because the Flood chose not to infect humanity... it was not humanities time to be "tested", it was the Forerunners time to be tested. Humans would be tested next, after the Forerunner were destroyed.
Until theire defeat at the hands of humanity, the Flood were viewed as an unstoppable force. Humanities victory gave the Forerunner hope they the Flood could be defeated... they just needed to learn humanities secret. But this knowledge turned the victory into a hollow one. Humanity had defeated the flood simply because the Flood were not trying to win. Their target were the Forerunners.
This had huge implications for the rest of the Halo universe. As discussed previously the Didact was opposed to the Halo rings. He believed the Forerunners were capable of holding off the infection with military might just as the Humans had done. But now he new humans hadn't really defeated the Flood. That is why, after trying every other means at his disposal it was the Didact that chose the fire the Halo array wiping out the universe of Sentient life. In addition, the knowledge that humans were the next species to be tested is what led the forerunner to set humans up as their inheritor. Humanities status as inheritor is what made the Prophets hate humanity, and it is the reason they were determined to destroy humanity.
There is a second theory about the Flood and the Precursors. Instead of being a Precursor weapon, the Flood were their enemy. Before turning their sights on the Milky way Galaxy is is possible the Flood had taken over what-ever Galaxy the Precursors had called home. That would explain why the Forerunners were able to push the Precursors from the Galaxy - perhaps the Precursors where weakened by the Flood infection. Having destroyed the Precursors galaxy, the Flood attacked our Galaxy.
Either explanation seems possible, though the fiction is certainly pointing to the idea that the Flood was a Precursor weapon sent into the Galaxy to destroy the Forerunners, and eventually humanity. I would imagine the trilogy of games that begins with Halo 4 will begin to point to which theory is correct... or even point in an entirely new direction. Either way it will be fun to uncover.
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