The Region of Alleos has recently opened it's doors back up to the public after realizing that they can't stop the chaos within their own region. The Belltower Company has formed to annihilate all the Pokemon in existence along with the people who support Pokemon.
Pokemon are not as they were portrayed in myths and legends to children, they're human eating beasts who can shift between a Pokemon and human esque form, known as a Gijinka. It's rumored that legendary Pokemon are forming together to create a Pokeball to capture humans and use it to farm them like cattle.

You'd better start chasing your spirit.