This tells the tale of Lillie, an up and coming trainer, meeting with Red, a revered Pokemon Master. Red takes on Lillie as his apprentice, and together they fight to make the Pokemon world a better place.

This story takes place after the events of all the Pokemon games. Red has accepted his rightful place as Champion of Kanto, but the world is just not right. The other regions are beginning to forget what it means to be a true Pokemon Trainer. Red must then battle against iconic trainers such as Brendan and N, in order to set them on the right path once again.