One day, the legendary pokémon Mewtwo and Arceus combined their powers to free every pokémon on the planet from every pokéball and PC, as well as giving them heightened intelligence to the point where most pokémon can speak human languages 
The now free, pokémon turned on humanity. Destroying human society in mear days and culling more than half of the human population in two years.

Pokémon are, at best, intolerant to humans, but still see them as prey, playthings, and vermin.