The story of FireRed LeafGreen begins with Green ready to meet her parents, but they are drawn into a spiral that creates a mysterious Pokémon! Red and Blue want to help, but first, they need to improve their battling skills. Then, the Three Treasures of Team Rocket return with their usual plans!

In the story of Emerald, Gold and Crystal are back again! Professor Oak sends the two friends to help rescue Red, Yellow, Blue, and Green - who have been turned to stone! But first, the pair must battle a terrible creature that Archie, the former leader of Team Aqua, wished to create using the powers of the Wish Pokémon Jirachi!