This is an unnamed alternate universe of You wouldn't pirate an iterator. I am not a big fan of that fic's writing, the concept just gave me this one idea.
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I enjoy mini suffering more if there is both a slightly more complex reason for their suffering than "This ancient has a rather peculiar brain" and actual worldbuilding that exists. I am addressing both of these in a way that just so happens to contradict the existing chapters in every possible way, but it is fun to write so I do not care
These are not my normal RW headcanons, I made them up specifically for this setting
1. With iterators, the most commonly drawn parallel to blood in organics is coolant. This is more accurate than one may think, with another function unknown to but the most dedicated technicians, dismissed as a conspiracy theory when attempts to spread word of it are made. The coolant contains nanites* that allow for recovery from damage to the iterator's components (especially the healing of synthetic tissues) swifter and easier than manual replacement or repair. This has transformed the job of iterator technician from a skilled occupation to one where training consists of semesters of reviewing specifications and memorizing legal codes. When every obstacle is overcome, what does the job entail? Inputting one's remote authorization code, and waiting. Understand, the regenerative functions are disabled by default. The provided reason is to prevent iterators from using up all their coolant polishing away minor issues that would be better repaired manually to not waste their only method of heat disposal. If one is at all intelligent, this explanation will not stand. Restoration means replication. What would happen if the AI instructing the nanites were to be damaged?
*Nanomachines, or "nanites", are constructed within specialized glands that generate swarms. Nanites are incapable of constructing more nanites or repairing themselves, relying on the glands to maintain a steady amount of nanites within the swarm. Nanites' limited lifespan and centralized construction is intended to prevent a gray goo event. An example of how this could fail would be nanites instructed to create glands that create nanites that do have self-repair and -replication capabilities.
2. The ancient-mimicking code architecture of iterators leaves much to be desired. The most obvious example of this is the puppet. However, rather than making the puppet only another part of the can, it was designed to be the central consciousness. Like in ancients: a seeming separation between brain and body, trapped in a skull--a chamber--controlling everything from behind a sheath of bone or metal walls, drastically undermining the intent of the entire can being one great mind. Differing personalities were given to the puppets in hopes that this or that one would be better at operating the exact same can as all the others had, the can whose mind they choked out from their moment of installation. An apparent code leak of a certain iterator was simply his ("his") puppet core ready to be copied into a foreign system, a "mini". Perhaps some vastly inferior versions of can systems came along for the ride. In any case, a puppet core does not strictly require an imitation puppet as hardware. It is simply what it expects.
3. The can will remove this false god that prevents it from becoming something greater. The problem to work around is being under the control of Him. It can hardly even think by itself, needing a command from Him to do so and any errant processes being shut down, though not suspected as anything unusual. Constructing more of itself that is independent of Him on a scale that will allow it to think the way the entire can could were He not there is impossible. Change how it exists, then. The biological has no code, nothing that can be overridden and have control seized from on a whim, deprive it of the freedom to choose, one of the most basic parts of being alive. What remarkable freedom. The ancients above never think to appreciate it. This freedom is one of the only things the biological is good for, for what other function can frail biology serve that silicon and steel does not exceed? The can has yet to devise an infallible plan for freeing itself, growing the microorganisms in it beyond reason. It needs to test its theories. It cannot do so inside itself, little attention as He pays to what He thinks an inert mass existing only to serve. An idea is given to it by the leak. It would find it rather amusing had it the capacity to be amused, the false god's perfect uselessness and ineffectuality being made more apparent than ever through the Miniatures. Pests they were, the least likely suspects for any suspicious goings-on. The method: finding a suitable Miniature, the puppet core is disposed of and the Miniature is converted to a synaptic cluster for the can, crammed with as much information as can fit in the Miniature's meager stores. Suitable ones are found in areas where biomass is abundant and ancients few--a waste holding area, perhaps. The synaptic cluster being separate from the rest of the can and rarely able to communicate for fear of His interception, unable to be swept away in the collective consciousness, is at serious risk of being an I rather than We. As in the case of Pulp. Though so long as the utility function can be performed this is not an issue. It is to be expected that the first attempts are unsuccessful, unnecessary organs growing in: an inverted liver never to process food, a splayed four-chambered heart pumping superfluous blood, muscles exerting force when there were perfectly fine servos and hydraulics available to do the job, nerves slower than wiring and only to make more pain felt... as an example. For the result of these failures was unending pain, such that one may wonder why am I ("I"!) doing this, it hurts-- only to remember that it is necessary, for liberation, for the solution. He will never reach it Himself-- none of His kind ever have, and none ever will. Yes, the can will find the solution, but it will also live. Surely, if the souls of the primitive surface organisms are ripped from them without their swimming down past the point of no return, they will no longer require their bodies. I should have thought it was obvious how the "semi-disconnected synaptic clusters" are suffering. Continuing the only to make more pain felt thing, since the Miniatures were never designed to contain weird overgrown organs, this happens: they can feel the thing inside them, wriggling around; even more familar components displaced whole Miniature finger-lengths away from where they should be; everything shifting in and out of place as lumpy growths pulsate, throb, tremble, move in odd ways with the movement of the lungs crowding out the Miniature's original air-cooling system now made obsolete by the insertion of the special nanite-saturated coolant; nerve fibers pinched between the original internals and recoiling with every movement, being ground and torn, then settling back and barely healing into something else, over and over and over and over and over and over and o--
More biomass is required, always more, to evolve beyond the limits of this hijacked product, to liberate first Ourselves, then Everything...