After having a fated dream, Haruka encounters a mysterious Pokemon called Manaphy, who claims to be the 'prince' of the sea Pokemon. Little do they know, an evil pirate named "Phantom" tries to kidnap Manaphy, as Manaphy is the key to a hidden ancient undersea temple "Ackeusha", which once belonged to a water-based civilization, was able to comminucate with Pokemon by mind. Now its up to Satoshi and company, and their new friends Hiromi, a descendant of said civilization, and Jack "Jackie" Walker, a Pokemon Ranger, to protect Manaphy and stop the evil pirate from claiming the power hidden within the temple.