Satoshi journeys to Alto Mare with companions Misty and Brock. During a local water race, he catches a fleeting glimpse of an invisible Latias before crossing paths with antagonists Annie and Oakley, who attempt to seize the Pokémon. He guides Latias to safety following this skirmish. Driven by curiosity, he visits a museum where curator Lorenzo reveals Alto Mare's history and the Soul Dew artifact. Later, Satoshi pursues Bianca across the city into a concealed garden sanctuary inhabited by Latias and Latios, witnessing Pikachu interact with the Eon Pokémon.

When Annie and Oakley capture Latios and steal the Soul Dew to activate Alto Mare's Defense Mechanism (D.M.A.), Satoshi leaps into action. Latias escapes the antagonists and seeks his aid. After the D.M.A. activates and revives fossilized Pokémon, Satoshi and Pikachu join forces with Latias to infiltrate the museum. They confront the antagonists to disable the weapon and free Latios. Amid the struggle, the Soul Dew shatters, unleashing a colossal tidal wave that imperils the city. Latias and Latios unite their powers to halt the wave, but Latios perishes in the effort.

Before departing Alto Mare, Satoshi encounters a mysterious girl resembling Bianca. She hands him a sketch depicting him and Pikachu, then silently kisses him before vanishing. Satoshi, Misty, and Brock resume their journey.