I believe there’s one specific passage in Halo: Cryptum on page 157 that re-contextualizes everything the Flood’s done into one coherent set of motivations and goals.
There is requisite context for the interpretation of the passage which is diffused throughout the three novels of the series.
1st: The Didact at this point in the story is already afflicted with the Logic Plague, having conversed with the Primordial.
2nd: The Logic Plague is transmitted through interaction… the transfer of information… and there’s no more significant transfer of information than a Forerunner serving as the template for another Forerunner’s mutation. As such Bornstellar now carries the Logic Plague from the point of him undergoing his first mutation.
3rd: The nature of the Logic Plague is that it is grafting the mind of the governing intelligence behind everything the Flood does onto the mind of the recipient, enabling it to manipulate the thought processes of the recipient in both subtle and obvious ways.
4th: the quotation is given through Bornstellar’s senses, informing the reader of what Bornstellar perceived, as he perceived it.
Now for the quotation:
For a few minutes, I thought I experienced yet another voice in my head, not me, not my past me or any future me. It seemed to contain a great deal of knowledge, none of it any use. It was knowledge that belonged to others from very far away, other existences where life and death were meaningless, light and darkness twisted together, where the twin fists of time uncurled their fingers and joined in a clasp, so that nothing changed or ever would.
That last part is the most important part. It’s describing eternity. Literal existence completely disconnected from the flow of time. The past and future (the “twin fists of time”) existing simultaneously and perpetually, eternally unchanging, is the nature of the mind Bornstellar observed.
That is not consistent with any type of mortal being that can be killed or driven insane. If that passage is literally accurate as it appears to be, then the entirety of what the Forerunners thought they knew about the Precursors is completely wrong.
As eternal beings, the Precursors are not subject to the flow of time, which means they were not eradicated, were not desperate to preserve themselves, and they knew the dust would turn into the Flood. All of it is known from the beginning, and was permitted or orchestrated as part of a larger plan. That larger plan is the Mantle of Responsibility.
The Mantle of Responsibility is the duty of the chosen race to safeguard the oportunity of all other races to the reach their highest potential. Not to lead them, or to police them, merely to prevent them from being perpetually prevented from the development they were designed to undergo.
The race the Precursors created to inherit the Mantle was Humanity, but at some point in the distant past, Humanity split into two factions. One that became the ancestors of modern humanity, and one that spent more than ten-million years genetically altering themselves, splicing the genetic strengths of other races into themselves into an attempt to turn themselves into the ultimate species, these being the ancestors of the Forerunners.
The Precursors rejected the Forerunners, and chose Humanity, because the Forerunners were already showing that they didn’t understand the Mantle, and were violating it in their attempts to enforce peace on the galaxy by preventing any other races from rising in power to the point where they could rival the Forerunners. The Forerunners exterminated the Precursors’ biological avatars they’d been using to guide the mortal races, and the Precursors turned the remnant of those avatars into the dust that would in time emerge as the Flood.
The Flood first emerged on human worlds, testing their worth, a test humanity passed by being self-sacrificial in their attempt to save the rest of the galaxy from the Flood. The Flood then stopped attacking humanity, creating the illusion that the “cure” worked, because if the Forerunners hadn’t believed that Humanity had a secret cure that the Forerunners couldn’t discover, the Forerunners would have exterminated humanity utterly. Instead, the Forerunners took special care to preserve humanity in the hope of eventually getting the “cure” from them.
The Forerunners analyzed the Flood’s abilities and realized that the Flood could have consumed everything long before the Halo Array was even designed, but it was deliberately taking longer to spread. In the context of the Mantle, it’s clear that the Flood didn’t wipe out the Forerunners immediately because the Forerunners hadn’t themselves reached their full potential. The end of Halo: Silentium highlights how Forerunner government is restructured, and the major changes they’re going through, exemplifying them finally reaching their peak, and it is at that point when the Flood stops holding back.
The Flood had experience with the Halos, and had even captured Halos from the first array. The Flood was perfectly capable of preventing the Halo Array from firing, but let it happen… but only after enacting judgement on the Forerunners, destroying the Greater Ark with the remnants of the Forerunner culture. This reset the galaxy, giving life a chance to prosper out from under the heels of the Forerunners, and without forcing the Flood to show its hand. Much later, the Flood emerged again, breaking the Covenant before it could exterminate the remnant of humanity, and then collecting its forces above the Ark, the only place in the universe where a Halo could be fired against it without civilian casualties.
The Flood is an antagonist (it does legitimately do terrible things to make the threat credible), galvanizing the mortal races through combat, driving them towards their potential, and towards otherwise unlikely alliances. The Flood is perfectly capable of winning quickly, but these new factions don’t know the extent of the Flood’s abilities, allowing it to hold back far more, giving them opportunities to plausibly “defeat” it. It’s pretending to be less powerful and more malicious than it is for the sake of driving events to the Precursors’ desired outcome.
The Flood isn’t actually trying to consume everything, but that’s the narrative it is perpetuating for the sake of manipulating the other races to the desired outcome.