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Every year the city of Alto Mare holds a special Water Pokémon race through its canal streets—and this time around, Ash and Misty are top competitors! Even though he doesn't win, Ash still finds his own special place in the heart of a mysterious girl that he rescues from two roguish women. But this isn't any ordinary girl—it's actually the Legendary Latias in disguise!

Ash gets a special peek into the secret world of Latios and Latias, but this world is soon threatened by the two women from before—Annie and Oakley—who are after the two Legendary Pokémon, as well as a mysterious jewel called the Soul Dew. These elements combined will let them control a powerful machine that normally protects against danger. When the machine malfunctions, though, it not only puts Latios and Latias at serious risk, but the entire city of Alto Mare!