The beautiful Alamos Town is home to a pair of century-old structures known as the Space-Time Towers, built by the architect Godey to play orchestral music in the area. The towers are also home to the Alamos Town Contest Hall, which is the next destination for Hikari, Satoshi, and Takeshi in their journey through the Sinnoh region. A woman named Alice and her partner Chimchar are happy to guide Satoshi and his friends through the town and its hallmarks. But the tour is suddenly interrupted when Alice's friend Tonio notices a wave of dimensional disturbances throughout the town—all of which is blamed on an ominous Pokémon named Darkrai. The space-time disturbances continue to intensify as two legendary Pokémon, the Temporal Pokémon Dialga and the Spatial Pokémon Palkia, appear to duel each other, isolating the town and everyone present in it from the world into another dimension! As he learns that this event was foreseen long ago, Tonio finds that his great-grandfather left behind a way to stop the dueling Pokémon. Will Satoshi and his friends be able to use this last resort to save Alamos Town from vaporizing between the dimensions?

The legendary Renegade Pokémon, Giratina, encounters the Temporal Pokémon Dialga by a lake and successfully manages to drag Dialga into its home—an alternate dimension separate from the normal world. But a small green Pokémon gets gotten dragged in as well—and though it somehow escapes, Dialga uses this opportunity to escape as well after preventing Giratina from chasing after it. After accidentally ruining Satoshi and his friends' picnic, the green Pokémon is taken to the Pokémon Center where it is treated for injuries and introduced as Shaymin, the mythical Gratitude Pokémon. Using telepathy, Shaymin demands that Satoshi, Hikari, and Takeshi take it somewhere. But before they can find out where to go, the group find themselves being pursued by both Giratina and a strange man named Zero—both in search of little Shaymin! Will Satoshi and his friends be able to find Shaymin's desired place while keeping themselves out of danger?

The Team Rocket leader, Giovanni, has found Mewtwo in a remote area of the Johto region. As Giovanni tries to re-capture Mewtwo, Ash and his friends are kidnapped by Domino, a new Team Rocket member, while trying to rescue Pikachu from Jessie and James. The Clone Pokemon are also captured and are then used as bait for Mewtwo. The situation then becomes a battle between the wills of Mewtwo and Giovanni; and Mewtwo also tries to discover if it and the clones have a purpose in life, even though they are products of science. (Source: ANN)

The anime tells the story of a boy named Akio and his encounter with a Hisuian Zorua. When he was younger, Akio's father taught him that people and Pokémon cannot live together. But Akio's interactions with the Zorua might offer a different lesson. (Source: The Pokémon Company)