The story of the game follows the main character Ash, a trainer from Pallet Town whose hobby is catching monsters. One day, he goes to Ciel Village where a boy named Bittercold awaits him with his friend Miki. Ash wants to catch a monster, but he doesn't know which one, so he asks Bittercold for help. They head to Ciel Village's Gym, where they encounter a mysterious girl named Latios who wishes to become a Pokemon Master. Latios then transforms into a new man that is now called Latiomystic.
Once Ash and his friends reach Ciel Village, Lati decides that he would like to become a Pokemon Master like his idol, Latios. He leaves to train alone in the gym but gets captured by Team Galactic. There, he is trained by Jirachi, a fusion of a black and white Dragonoid and a Dragonite. Team Galactic gives him the power stones that can transform into three different types of monsters including a Psychic, a Dragon and a Darkrai, and he can freely choose which type of monster he wants to be, though he can only change into the Psychic or the Darkrai.