The following information is conjecture and has not been backed or approved by Id Software. As such, it is subject to change.
Phase 1: Source acquisition
This is the acquisition of the biological frame from which the new Strogg is created. Some Strogg are gestated in vitro (refer to reconnaisance by Cpl. Bitterman, first wave, operation Overlord 2), but in combat, many are modified life forms, or "transfers." Sometimes the process is a hybrid, in which enemy biologics are rendered for organic substrate for use in the gestation of new Strogg bioforms.
Phase 2: Source preparation
Transfers are first injected with the nanoprep agent in a physiologically compatible medium with appropriate stabilizing agents. For humans, this is a normal saline base with corticosteroids. The nanomachines are similar in partial function to those in health packs, but far more versatile and advanced. Next, unnecessary biomass is removed from the transfer prior to first augmentation. In most cases, this includes both legs and one arm. All waste product is routed to processing and putrefaction for processing into either organic slurry for materials production or stroyent (a substrate which, when applied to the nanobots, induces rapid tissue growth and repair).
Sometimes preparations are more radical, removing all limbs, all limbs plus the pelvis, or even removal of the brain, depending on the Strogg to be generated. However, at this point the organism needs to at least be compatible with life.
Phase 3: First Augmentation
At this stage, the organism, still physically restrained, is fitted with cybernetic connection points which connect the organic parts to the cybernetic augments. In some cases, these connection points include the augments already. Some Strogg are generated to near-completion at this step. Others are fitted prior to the next phase in order to attain completion at phase 5.
Phase 4: Integration
This is the implantation of the neuron-cybernetic integration system (neurocyte chip) into the central nervous system of the transfer.
Phase 5: Activation
This requires detailed mapping of the peripheral and central nervous system with information written to the neurocyte (also known as Neurocyte Registration). This information allows the neurocyte to then sieze control of the central nervous system outside of the conscious control of the host. This is the threshold, the effective "point of no return," as higher neural functions may atrophy as the host mind just "gives up." However, if the transfer is removed from stroggification before mapping of the cortex is completed, the host retains control of their body. It should be noted that it is theoretically possible to remove the neurocyte, but the estimates of risk are high. Once activated, there is a limited amount of time within which it is theoretically possible to deactivate the neurocyte. However, this must be done quickly. It is unknown just how long it takes before a transfer becomes non-salvagable.
Phase 6 (depending on design of strogg to be produced): Second augmentation
Some strogg require more radical reconfiguration, and, once activated, are sent to undergo more radical alterations. Sometimes these alterations remove all tissue down to the brain, placing the brain inside a host machine (seen in the "repair bots"). Tissue remains are either recycled whole, used intact in other bio-cybernetic support systems, or discarded. If discarded, they are routed for use as feedstock in the production of organic substrate materials, including in vitro culture media for Strogg bio-bodies, various reagents, or the stroyent repair compound.
Now that you've waded through my imaginary technical mind (interpret that phrase, I dare you), here's the good news. The next episode of Kane's Mind is now complete. As I write this, Windows Live Movie Maker (yeah, I still haven't found the spare cash for Sony Vegas) is publishing the episode to YouTube. The process will take a couple of hours, including frame rendering, uploading, and YouTube server-side processing, and since it's late and I really need some sleep, you'll get to see it on YouTube before I even get to finalize the description or put the link on this site.