Kanto and Isshu have let their nuclear weapons fly. Only one out of every four people from the old days have survived, and they do so against a backdrop of anarchy and nuclear winter. Pokemon trainers have become warlords. Trainers challenge you on the roads not for a friendly battle, but to steal your food and pokemon. Legendaries wreak havoc and the priests are calling it Arceus' judgment - unless you're brave and crazy enough to try to catch them, and skilled enough to succeed.
Oh yeah, and Giovanni's dead, so are the Elite Four, and Team Rocket's more popular than the Pokemon League.
You are a survivor. You have made it through the first five years of the worst era in human history. Maybe you were a skilled trainer even in the old days, or maybe your pokemon have grown strong and evolved from the struggle to survive. Or maybe they haven't, and you're just a kid starting on your journey with a level five Bulbasaur, trying to keep the dream of the old days alive.