Kanto has always been a paradise of sorts. Mild weather, beaches, beautiful forests, and people and pokemon living together in harmony. Then things began to change. The first sign of trouble was the loss of the passenger ship Helios. It sank on a trip from Vermillion City to Slateport. Although there were no survivors the last transmission from the ship said they had been attacked by pokemon. Within the year, travel between the islands by sea was almost impossible. Any ships attempting the trip would be attacked by dozens of crazed water pokemon. Trade came to a standstill, and the ports were closed.
Then the problems started with the more terrestrial pokemon. Wild pokemon became more aggressive, exhibiting odd behaviors and attacking any humans they saw. Then their physiology began to change as well, they would evolve into odd misshapen forms with extra limbs, odd coloring and other mutations. Soon even domesticated pokemon became affected, attacking their masters and running off into the wilds.
That was almost a decade ago. Now travel between even neighboring cities is a dangerous activity. Trade has dried up, food has started to become an issue, and people are struggling just to get by.