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 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.

A century ago, the power of a mighty creature known as Hoopa, who is capable of single-handedly defeating legendary Pokémon, was captured in a bottle by a lone traveler. The bottle was then hidden deep inside a cave in the desert, in the hopes that the darkness sealed within it would never see the light of day again. Years later, a young man finds the bottle and breaks the curses surrounding it, releasing the power confined within it. Its contents take the form of Hoopa's shadow, and it uses its unbound power to shatter the bottle and prevent anyone from capturing it again. The shadow then goes on a rampage and attacks the original Hoopa, while both Pokémon summon other legendary creatures to aid them in their brawl. Satoshi—a budding Pokémon trainer from the Kanto region—and his friends are caught up in the crossfire, and must now work to stop the ravaging Pokémon, or face a devastating clash of legends.

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)