How Does PC Storage Work? Edit
The world was revolutionized by technology that could convert matter into data. As this breakthrough trickled down to the average consumer, unimaginable progress gains were realized. Trainers got the ability to store their inventory on a home computer and then retrieve it from any computer that had sufficient bandwidth to transfer the item. And for vending machines, instead of having an internal storage of a few hundred items they could download a nearly limitless inventory directly from the factory. And backpacks can digitize their contents to local storage allowing a child to carry thousands upon thousands of items with ease.
We can see this a relatively new technology, and people still aren't entirely comfortable with it. Traditional moving companies still transfer the entire contents of a person's house via truck instead of simply emailing it as an attachment. Naturally, bandwidth required for such a move would be much higher than for a single item, and moving companies might have to invest untold fortunes in setting up the high-speed cables necessary for such mass transfers, but as this technology gets cheaper and more effective, we can expect it to work its way into virtually every facet of society.
Of course, one pioneer wasn't content to merely move items through the cables. This man, known simply as Bill, began working to transfer living things through the data pipelines. First plants, and then Pokemon, and then he moved on to human subjects. This is the source of the infamous Rattata episode in which his data got merged with a Pokemon's and were spat out as a single creature.
Nonetheless, such a system once perfected was a boon for early adopters, especially given the laws restricting trainers to just six Pokemon. Most only carried two or three in hopes of catching useful Pokemon, and often about the strength of the local wild Pokemon to ease catching. But those using Bill's system could send as many Pokemon to Bill's PC as the system could handle. Additionally, Pokemon centers which allowed free transfer of items could also be tricked into transferring Pokemon as well, digitally.
Science builds on science and it wasn't long before Dr. Akihabra managed to improve on Bill's work. It started with a simple question: if Pokemon can be converted into data and back, is it possible to turn data into Pokemon? The answer turned out to be yes. The first effort yielded a Pokemon he called Porygon, an entirely new artificial Pokemon.
How Do Pokeballs Capture Pokemon? Edit
Pokeballs were originally designed not to capture Pokemon but to store items for easy carrying. But when it turned out they worked on Pokemon they quickly were improved for that purpose and were known more as a capturing device than a portability one. Still, it's not uncommon to find a lost item stored in a Pokeball in some forgotten corner of the world.
A Pokeball turns a Pokemon into data for easy storage. While in a Pokeball, the Pokemon exists in a digital world. Humans can be captured as well, and as Bill and Akihabra among others have demonstrated, humans can travel to the digital existence. However, humans dislike the digital world. The experience is nearly impossible to describe, but it's common to hear phrases like "sterile", "uncomfortable", "pervasive wrongness", and "feels off somehow." Most Pokemon seem relatively comfortable there, but humans tend to bug out.
Pokemon can break out of Pokeballs as an act of will. Usually it's necessary to weaken them to reduce their resistance. Since humans have a stronger will than most Pokemon, they can easily break out of Pokeballs. Their discomfort in the digital world, coupled with horror stories about Bill's accident, have meant the failure of businesses which attempted to build transporters for humans, though some do their coding by being digitized and working on the system from the inside.
For a Pokemon, the Pokeball is programmed to create a digital environment that suits the Pokemon. If the Pokemon is known, the ball produces an environment that suits it. If the Pokemon is one yet to be discovered, the ball deduces its type and basic characteristics and produces an environment that is more or less fitting.
Part of digitizing the Pokemon is getting its ID, something akin to the ancient concept of a true name. This also functions as the filename that the Pokemon is saved under. A fainted Pokemon is not conscious, and thus not aware of who it is and so its ID cannot be read, and therefore the Pokemon cannot be caught and therefore throwing a Pokeball will fail. Previously captured Pokemon have their ID on file with the Pokeball and thus can be returned to their Pokeballs.
Thus, realizing this, players need never worry that they're killing wild Pokemon and that's why said Pokemon cannot be caught. No, it's simply a matter of a lack of ID. It's not until the Pokemon is left unconscious out in the open for awhile and a predator comes by and eats it that the Pokemon is dead.
How Do TM's Work? Edit
The first TM's were data disks that contained the instincts necessary for a Pokemon to use a particular technique in battle. The Pokemon would be returned to its pokeball and the disk would be placed on a spindle, turning in the pokeball as the pokeball's laser read the data off of it. The TM then uploads the data to the Pokemon directly, much like Neo learning kung-fu in the Matrix. These artificial memories and instincts need a bit of practice to become natural for the Pokemon, but thankfully the TM also modifies the pokeball's environment to include a training area to practice the move.
TM's require an intense amount of effort from a large team of programmers working for years on end. They are therefore expensive and the companies that produce them tend to include copyright protection to prevent duplication. Each TM is therefore one-use-only.
HM's by contrast have no such protection and can be used an unlimited amount of times. These are typically done for older moves that are not worth protecting in this way any more, or that the user is willing to pay extra for.