Two years after Phantom Planet, Danny has continued to protect Amity Park from evil ghost while balancing it with school life and his relationship with Sam. But when Clockwork comes to Danny with news about his future, danny must make big decisions about his life and accept The responsibilities of The Phantom King.

Young Lee McGowan is finally ready to set out on his own pokemon adventure, he heads to Professor Oak's lab with his best friend and travelling companion Jack Coulahan to receive their first pokemon, along the way they shall meet new friends and enemies aswell as slowly learn of a mysterious trainer that people all around the world refer to as "The Pokemon Master".