When Jack and Maddie Fenton, world famous researchers on Ghost Pokemon mysteriously vanish, the world was lead to believe that their son, Daniel Fenton, vanished along with them. However, the truth couldn’t be more different. Critically injured in the mysterious event that lead to their disappearance, Danny barely clung to life, and in order to survive and find his parents, he agreed to make a Pact with his mother’s Froslass, who was fading away from the same ‘accident’. This process, while saving his life, left the boy inescapably changed, transforming into a Human/Ghost Pokemon hybrid, although overall retaining his human shape. Gaining many fantastic powers from this change, Danny decided that he would seek out his missing parents and bring whoever kidnapped them and nearly killed him to justice. Taking on the alias of ‘Phantom’, he finds a clue when the local ghost Pokemon tell him that the mysterious and elusive Champion, Vlad Masters, knows something about his parents. But the only time anyone has ever seen Vlad was when they challenged him, meaning that Phantom would have to take on the gym leaders and the Elite Four of the Amity Region before he could do that.
Meanwhile, Danny’s best friends, Sam Manson and Tucker Foley, return at long last from their own Pokemon journeys, only to find that their best friend and his parents have vanished into thin air. Following a lead from Jazz Fenton, a Pokemon psychologist and Danny’s older sister, they start to seek him out, quickly crossing paths with Phantom. Not wanting to let his friends know who he is for fear of them rejecting him, Phantom nevertheless finds himself traveling along with them, as Sam tries to whip the incapable trainer into fighting shape. Meanwhile, the mysterious Team Plasmius is causing trouble elsewhere in the region, snatching up scientists, Pokemon, and artifacts alike, and knowing that they have something to do with his parents, Phantom and his friends come into direct confrontation with them. It seems that there are other people out there who want what Phantom has- and will stop at nothing to gain it.