Since the dawn of life, there have been four kinds of paths you choose at random when Arceus decided to create you. You could be an animal, a plant, a human, or a pokemon. Plants, for the most part, offered no resistance when used for sustenance or shelter, and where numerous enough that it was an understood fact it was impossible to eliminate them all, until of course the existence of modern technology, So that left Humans, Animals, and Pokemon. The three kingdoms of life in our world.
Animals were, of course, at the bottom, with little intelligence and often even fewer defenses, Humans easily hunted them down. And in turn the Pokemon, which had the advantage of both equally unique odd gifts of combat and were even smart enough to use basic tools, strategy, and communication, feasted upon the humans. As far as scientists can now tell, this was the way things were supposed to be. Animals at the bottom, Humans in the middle, and Pokemon at the top of the food chain.
That is, until, Humans realized something. They were easy targets, almost genetically so, as the original corner of the super continent they evolved from offered little protection when they were all clumped together, hundreds to a group and easy to track. So they spread out, and the Pokemon had a harder time searching for them, meaning they turned to other means of food, meaning that with the combined efforts of Pokemon and Humans alike they, unintentionally, wiped Animals off the map almost entirely before 50,000 BM (Before Mew).
Nowadays, Animals survive only in the forms of small worms, insects, and fish, but you'd never see the magnificent creatures you used too. There have been many attempts by modern paleontologists for us to attempt to rebuild the dna of many animals from what little we have of them, but that received push back from the public and press alike. Apparently they've now decided playing God is wrong. If only they got the memo before Mewtwo.
After the fall of Animals, Pokemon hunted Humans across the globe for thousands of years, but they were too few of them, and scattered so far, that Pokemon (who also lived in large clumps, much like us) were forced to eat eachother, least they seperate themselves from the tribe, which their instincts would not let them do.
After awhile, humans and Pokemon lived in relative peace, Humans were just smart enough to know when to keep out of range of Pokemon, and when to jump on one or two that had strayed from the pack in a desperate attempt to eat anything other than grained rice. Then, one day, Humans had to muck it all up again.
One man, who, while apparently searching for a way to filter water, accidently discovered gunpowder. Immediately, the people that discovered it used it to crudely make bombs out of, and proceeded to capture a group of pidgeys using a few well placed piles of gunpower, a lot of manpower, and a couple nets.
After a severe conditioning, the group of pidgey were sent all over the world with two messages in the ancient text of man, 1. How to make gunpowder, and 2. A declaration of War against all Pokemon for the thousands of years we spent running from them.
It is notable, that the following war, Between Man and Mon, while absolutely the bloodiest and longest conflict the world had ever known, lasting thousands more years with little evolution and with the sole purpose of eliminating the other group, was also the only recorded time in history that Humans ever all worked together against a single enemy, with all the same goal. Eventually, after domesticating a few more Pokemon (Oddish for food, Growlithe for hunting, Donphan for War) and slowly developing better and better guns, The Pokemon learned to retreat into hiding like Humans once did. Perhaps it was one too many genocides Kings would decide on a whim to commit against random Pokemon, or maybe it was the severe abuse and punishment they saw their brethren were being put through by us, but they learned. And when a Pokemon learns something. They don't forget it.
Even today, long after Humans have stopped killing the creatures as casually, and in such high numbers, Pokemon are still wary of us. Wary enough even that the reason a human travels into into a Pokemon den, even the most bloodthirsty creatures will usually not kill them, only maim or severely injure at worst. This is because a now innate fear of the retributions Kings would bring down onto entire colonies of Pokemon, using numbers, weapons, and strategy to kill Pokemon by the billions. Many of these Pokemon are extinct to this day, or refuse to come out of hiding.
Humans may never truly make up for what we did. And perhaps we don't want too. Because if we truly cared about making it up to them, then we probably wouldn't consider having them fight each other as a form of entertainment.
Just a quick little thing I wanted to write before bed. Don't worry, I'm still working on all my other stories, this was just something I had to write down. I have tons of other ideas, like why pokemon let themselves be controlled by humans, How smart I think Pokemon are in comparison to humans, what a life is like for a pokemon if they never get captured or meet a human (ie: What was their schooling like, their family structures?), or even how Pokeballs work. If you want to hear about any of that just let me know in the reviews.