Continuing their adventure in the Johto region, Satoshi and his friends arrive at Altomare, an island city known for its yearly Pokémon Water Race competition. While Takeshi and Kasumi take in the festivities, strange occurrences begin to happen to Satoshi—he inexplicably loses the race, witnesses some women attacking a girl with their Pokémon, and even after he and Pikachu save her, the girl later denies ever meeting them.
Fortunately, Satoshi soon understands the situation when he discovers that the girl he and Pikachu rescued was actually a Pokémon named Latias, who often takes the form of her human friend Kanon. Latias, along with another Pokémon called Latios, is known as the Eon Pokémon. Together, they protect Altomare along with a mystical blue orb known as the Soul Dew. An ancient legend of Altomare, deeply tied to the Eon Pokémon and the Soul Dew, is well known among the locals—and also to the sisters Zanner and Lyon, the thieves who earlier attacked Latias. As the criminals attempt to capture both the Eon Pokémon and the Soul Dew, Satoshi must step in to prevent catastrophe from befalling Altomare.