Nobody knows what happened. Frankly, those who do have died a long time ago. But the remains exist, telling a story of what had once been.
The story of humans that had lived along Pokémon.
Some say those people enslaved Pokémon because of their superior technology; others say that despite their technology, they were still able to overpower the humans. Very few claim that they lived together in harmony, battling side by side. There are only few remains of the humans and their technology in the forms of ruins and artifacts.
Pokémon were still not able to grasp their technology, some even being afraid of it and saying interacting with it brings bad luck. Commonly those who showed interest are quickly cast out of society, so that no misery may come over their village.
What caused the extinction of the Homo sapiens? Nobody knows for sure. However there is one thing everyone seemed to be sure of, it has to do with the wastelands; corrupted lands with no plant life and deadly sludge.
Life would be impossible there, however, as it seems very few Pokémon were able to survive the harsh conditions and whatever happened there made them mutate.
Everybody was afraid of them, saying they bring chaos and destruction. Luckily, a mountain chain was separating the wastelands from the rest of the world. For additional security, elites are trained to defend their home against potential trespassers.
It already had been like this for thousands of years. The mutants who tried to leave the wastelands got killed mercilessly. Nobody gets through, mutated or not doesn't matter, it's the law.
However, sometimes, someone snuck past the guards allowing them to enter the other lands, commonly young Pokémon want to see if the story of the wastelands are true and dare to wander around close to the border. Rarely a mutant gets through, hoping to find a village to destroy, or so they say.