As they continue their journey through the Johto region, Satoshi and his friends visit Altomare, an island city that hosts an annual racing event called the Pokémon Water Race. While Takeshi and Kasumi are enjoying themselves, strange things seem to be happening to Satoshi—he somehow loses the water race, sees some women attack a girl with their Pokémon, and despite them saving her, the girl later denies ever seeing Satoshi and Pikachu before! Fortunately for Satoshi, his confusion clears up as he learns that the girl he and Pikachu saved earlier was actually a Pokémon named Latias, who likes to disguise herself as her human friend, Kanon. Latias and another Pokémon, Latios, are known as the Eon Pokémon, as they inhabit and guard Altomare along with a mystical blue sphere called the Soul Dew. An ancient legend of Altomare is highly connected to the Eon Pokémon and the Soul Dew, and is well known among the locals—as well as among Latias' earlier assailants, the thief sisters Zanner and Lyon. As the thieves attempt to capture both the Eon Pokémon and the Soul Dew, Satoshi is forced to act in order to stop them from bringing disaster to Altomare.

High-tech LaRousse City is a pretty impressive place to visit—and a pretty impressive place for a Pokémon battle, too! Satoshi heads straight for their renowned Battle Tower, but things don't turn out too well when his battle partner turns out to be a scared boy named Tooi. Because of a frightening childhood incident, Tooi is scared of all Pokémon—even cute ones like Pikachu! There's a lot more to be frightened by when Deoxys shows up and takes control of the city, shutting down the machines and taking everyone captive. One Pokémon that is not amused is the Legendary Rayquaza, and it will do whatever it takes to remove this invader from its territory! Meanwhile, Satoshi, Tooi, and all their friends may be caught in the middle, but they're certainly not out of the fight! (Source: Official site)

The Millennium Comet is about to make its long-awaited appearance in the sky again, supposedly granting the wishes of all those who see it in the skies above them. Of course, Satoshi and friends are equally interested in the Millennium Festival, especially when they attend a magic performance by the Great Butler. Even more interesting is the mysterious cocoon in Butler’s possession—from which Masato hears a mysterious voice calling! When Jirachi emerges from its slumber, Masato has a new friend—sadly, it’s only for the brief few days that the Millennium Comet appears in the sky. Masato is anxious to make the most of his time with his new friend, but the Great Butler has his own plans for Jirachi, which are not so friendly. He wants to revive the Legendary Groudon, and Jirachi just might be able to grant that wish. Can Masato, Satoshi, Haruka, and Takeshi stop Butler and save Jirachi before Groudon reappears to reign destruction over the land? (Source: Official site)

Serebii, a Legendary Pokémon known for its ability to traverse time, is hunted by an unnamed Pokémon poacher seeking to capture it. Yukinari, a young Pokémon trainer who enjoys drawing portraits of Pokémon, tries to protect Serebii after it stumbles upon him; but in the middle of its escape, both vanish without a trace. Forty years later, ambitious Pokémon trainer Satoshi hopes to sight rare Pokémon around his local area. White, a boat driver, takes Satoshi to his village. Satoshi is accompanied by his three closest friends: Takeshi, a former gym leader training to be a great Pokémon breeder; Kasumi, a young girl wanting to become a skilled Water-type trainer; and Pikachu, Satoshi's Pokémon partner and first comrade. Meanwhile, Yukinari and Serebii reappear in Satoshi's present time and run into his group. Masked Lord Vicious, the strongest executive staff member of Team Rocket, desires to capture Serebii. Using the Dark Ball, a variant of Monster Ball that corrupts the Pokémon caught within and draws out their maximum power, Vicious can transform innocent Pokémon into powerful and frightening obstacles—including Serebii itself! Placed in a tough position, Satoshi, Yukinari, and their friends must work together to defeat Vicious and save Serebii and themselves.