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And then, a third metamorphosis had taken place.
Deep within the Flood Super-Cell were memories coded in endless streams of genetic material, memories that spanned the galaxy, encompassing millions of worlds. The information was uncountable orders of magnitudes above what it had already categorized, beyond what it could process before the Universe died.
But there was no chaos, no disorder. The memories had been impeccably ordered by itself a hundred thousand years ago, and the knowledge relevant to its situation was easily found. The strategies and assessments it had made minutes before were reevaluated, updated, discarded often. The simpler intelligence had done well enough, but there was much it hadn't known, did not understand.
With a hundred thousand eyes, it peered into the space surrounding this Forerunner abomination. It extended its awareness to the warships of the self-styled Covenant, warships that would soon ferry it to the furthest reaches of the galaxy. Throughout the history of the universe, on the rocky shoals of distant worlds, species which had just acquired the gift of sentience had also gazed into the night sky. Unconsciously recognizing their inability to comprehend the scale of the universe, they often dreamed of an entity, or many such entities, that could.
Taking their deities in hand, the manifold species would then ascribe to them the role of creating the universe, and more importantly, of creating the species themselves.
What did they know of creation?
Deep within the warship that the central intelligence occupied, and within entrenched defensive positions abroad, the simpler intelligence had instinctively stockpiled hosts that were unfit for use. Devoid of their knowledge, they were nothing more than configurations of biomass, designed for the role of survival.
More efficient configurations existed.
Under its direction, biological machinery delved into the stores and rendered the bodies down into the base proteins and acids. The Flood Super Cell was introduced and multiplied throughout the biomass. Designs that had been honed by centuries of war were brought to the fore. It called extinct creatures into being, gave them form in its own likeness and granted them purpose.
One after another, the crucibles broke. A multitude of creatures spilled forth, creatures designed for supreme resilience and mutability. As the old ones spread and advanced toward their objectives, as hosts were recalled to fuel new furnaces and be made anew within new crucibles, the agents of the Fortress-World struggled to seize the initiative. Biomass was burned before the Flood could reach it, and the crucibles were sought out with surgical strikes.
Futile.
A hundred thousand years of solitude, and strange eons before even then, had taught it ultimate patience. Deep within prisons constructed for it, it had lain dreaming of vistas as vast and empty as interstellar space. But unlike the Monitor of this Halo, time had not dulled its wits, and entropy had not sapped its will.
Three factions lay before it, warring with each other more than they fought the Flood. Two were isolated and unable to call for help, the third a victim of time and neglect, and yet they sought to return the Intelligence to its prison? Silence it for ages yet to come?
I think not.