You start out at PokéMountain, a peaceful place. You live there, as a (___). You live with your master, Hihidaruma (Will probably change). And he's helpers, Shimama, Vigoroth and Sentret.
Then your island lands under attack.
A Darkrai is leading a group of 1001 PokéKnights.
They convert most of the MANY Pokémon on your island.
You are told by Hihidaruma to go around the island and recruit the lost and converted Pokémon to help the city. You have some choices to make in the game, like recruit Seedot or Makuhita. It will have many loopholes and twists.
List of Recruitable Pokémon:
Seedot or Makuhita (You have to pick)
Shiftry or Hariyama (The one you didn't recruit is recruitable much later in the game)
Latios or Latias
(Will add more.)