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.

The homeland of the Genesect exists no more. After three hundred million years, the snowy mountains where the Paleozoic Pokémon once lived are no longer habitable—but not all of the race are actually extinct. Several specimens are still alive and desperate to find a new place to call home. Led by a Shiny Genesect and accompanied by the Legendary Pokémon Mewtwo, the vagabond creatures arrive in New Tork City. Perceiving the city skyline as similar to their initial habitat, the Genesect take over the city center, driving out other Pokémon and threatening the existence of the local populace. On top of that, the Genesect leader confronts Mewtwo in a cunning, fast-paced duel that is bound to destroy the entire city—and it's up to Satoshi and his companions to save the city and reconcile the feuding Pokémon.

As Satoshi continues his journey to become a Pokémon Master, he travels to Fura City to attend the annual Wind Festival. Pumped up, Satoshi and Pikachu are determined to win the festival's Get Race. Meanwhile, Kagachi, a show-off and a habitual liar, joins the competition at the request of his niece Lily. Having almost no knowledge about Pokémon, he manages to strike a deal with a socially awkward scientist named Torito in exchange for help with his upcoming speech. Following Kagachi's victory, Satoshi meets Risa, an ex-regional track and field champion looking to catch a Pokémon. However, during Torito's speech, Team Rocket strikes and manages to steal a capsule from his lab. Tragedy strikes one after another as the Wind Festival's Sacred Flame disappears! As they set off on a journey to find the culprit, Satoshi and the group meet many people on the way—including Zeraora, the Thunderclap Pokémon who was believed to be dead...