The Pokémon anthromorphication process, also known as Pokemorphing or The Change, begins with selecting an eligible Pokémon. Most species of Pokémon are compatible with the procedure, though a few require additional or altered procedures.
The Pokémon is first examined for sickness or any extensive injuries that may complicate the procedure. Normally, if a Pokémon is discovered in a condition that would complicate or make impossible the procedure, the Pokémon is moved out of the Armageddon Project or discarded. If the Pokémon passes the basic health and fitness checks, the next step is to select the human DNA that will be used for this particular Pokémon.
Most often, a Pokémon selected for the procedure has been trained by a Team Rocket agent, at least for a time. For reasons as of yet unclear to the scientists of Team Rocket, using the Pokémon's trainer's DNA results in a higher success rate for the process. However, there are cases in which the Pokémon had no trainer in Team Rocket, or the trainer does not possess the desired physical or mental attributes to pass onto the Pokémon. In this case, another human's DNA is selected with the desired characteristics. A small DNA sample, generally a few red blood cells or a skin sample, is then added to an amount of Agent Armageddon.
The exact composition of the Armageddon Agent changed between the First and Second Generation, but the basic elements are the same. A mutagen is designed simply to slowly break down the Pokémon's cells, and force the Pokémon's body to heal itself. Nanomachines are programmed to detect and read the human DNA in the Agent, and reconstruct key parts of the Pokémon's own DNA to match. This results in the healing done by the Pokémon to reconstruct according to the new template, rather than the original Pokémon DNA that would normally be used. Finally, a concentrated form of the Potion medicine used on Pokémon allows the Pokémon to heal more rapidly, and increase the likelihood of the Pokémon surviving the procedure.
The Pokémon is first sedated, and then injected with the Armageddon Agent, which begins to take effect within the first hour. The sedation typically wears off during the first day of the procedure, but the damage to the Pokémon's body, even at the early stage in the procedure, prevents it from functioning in any useful way. The Pokémon often drifts in and out of consciousness from this point forward, and though it has yet to be proven that Pokémon are lucid at this point, many Pokemorphs completing the process recall indistinct, hazy memories of burning and tearing pain. Attempts to keep the Pokémon sedated for longer than the initial period of time have universally resulted in the procedure failing.
In order to prevent the Pokémon from quickly dying of shock or failing of vital bodily functions, the process takes over a full week to complete, even with the improved methods of the Second Generation. During the latter half of the procedure, the Pokémon is classified as a Pokemorph, and no longer a Pokémon. The Physical changes are mostly complete at this point, though minor physical changes will still occur until the end of the procedure, and to an extent, afterwards, as well. During the latter stages of the procedure, the Pokemorph is moved into a stabilization chamber while the Pokemorph's brain is altered to become more human-like. The chamber is filled with a fluid that is absorbed through the skin, containing vital nutrients and chemicals to stabilize the new physical form of the Pokemorph.
The procedure is considered complete when the new Pokemorph regains full consciousness. The Pokemorph is typically weak and disoriented at this point, unaccustomed to its new body, and unfamiliar with the way its mind is now able to function at a higher level. The fluid is drained from the Pokemorph's chamber, and the Pokemorph is cleaned. During the First Generation, the Pokemorph was then immediately clothed and started in training in basic mobility in its new body and speech. During the Second Generation, the Pokemorph is typically allowed to orient itself and rest for two days before beginning training.
At this point, the Pokemorph is fully functional, but may continue to experience pains from final, normally imperceptible changes to its body. The nanomachines are completely shut down, and they, as well as the other components of the Armageddon agent, are mostly filtered out by the Pokemorph's liver.
First Generation issues
The First Generation nanomachines, notably, to leave a number of themselves in the Pokemorph's body tissue, and are sometimes activated by the electrical impulses in the Pokemorph's body. The activation only causes a short-range radio transmission from the nanomachine, which originally allowed it to communicate with other machines. It has no effect on a Pokemorph normally, but makes evolution into a Dark-Type, such as Eevee to Umbreon, a difficult and normally fatal transition. This problem was resolved in the Second Generation.
Team Plasma alterations
Team Plasma, upon stealing the basic Second Generation version of Agent Armageddon, made some changes of their own before beginning their main Morphing operation. The major change made is that, due to slowing the morphing procedure to take a longer period of time, and caring humanely for the subject with applications of various pain-killers and closer monitoring of their condition, the procedure is less traumatically painful. That isn't to say it's painless; The Pokemon in question is still having their entire body broken apart and reformed, tiny bit by molecular bit, but it's not as fast and less brutally painful than the Rocket morphing process; as the goal isn't speed, but more comfort. Furthermore, Plasma gave Pokemorphs as much time as they needed (within reason) to get adjusted to their new forms, as well as post-morphing treatment such as pain killers, sleep aids, and physical therapy, to ensure that Pokemorphs, upon beginning their new lives, were adjusted and comfortable with their new bodies, rather than thrust into action as soon as feasibly possible.
As a footnote, some Pokémon do require variations on the procedure. Ghost-Type Pokémon, in particular, do not have a traditional biology, and instead are infused with the Armageddon Agent in vaporous form. The Agent attaches to the Pokémon in that manner, and the process continues as it normally would. Similarly, Porygon Pokémon have a digitized version of the Agent run on them as an application. Similar results ensue.