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?

In ages past, the Kingdom of the Vale, a mighty and flourishing realm, fell into turmoil. The ruler's two sons turned against each other, unleashing the powers of their Legendary familiars—Reshiram and Zekrom—and disturbing the Dragon Force that supplied the kingdom with energy. With the help of the Mythical Pokémon Victini, balance was restored and the Dragon Force was bound by the Sword of the Vale. Should the Sword be moved, devastation will loom again. Damon, a descendant of the now scattered People of the Vale, is attempting to restore his people's kingdom to its former glory. He manages to summon Legendary Pokémon Zekrom, with the aim of lifting the Sword of the Vale and harnessing the power of the Dragon Force himself. Meanwhile, Satoshi and his companions visit Eindoak Town, located at the foot of the Sword of the Vale. Confronted with Damon's scheme, they lend a hand to Victini, guardian of the Vale, in stopping the plan from coming to fruition and preventing a repeat of the tragedy that occurred a millennium ago.

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)

Satoshi and his friends get lost in an unknown wasteland. They eventually come across a Water Pokemon Show performed by the star of the Mariner Troupe, Hiromi. Hiromi is a descendant of the troupe of Water People able to communicate with water pokemon, and she tells our heroes the legend that's been passed down by her people for generations. According to legend, a temple the Water People built called The Water Temple Akuusha rests somewhere in the ocean, and a treasure called The Water Crown is hidden there. It's said that no one has ever seen this treasure, but that changes when a Pokemon Ranger named Jack Walker (aka Jackie) appears to chase aftert it. Jackie is on a top secret mission that has him protecting the egg of the leader of the water pokemon, Manaphy. This pokemon, called the Prince of the Sea, needs to be taken to the Water Temple Akuusha, so Satoshi-tachi and Hiromi decide to help him. Along the way, a pirate named Phantom attacks our heroes from his great submarine. Phantom plans to use the Water Crown's power to help him conquer the world, but he'll have to solve the mystery of Manaphy's egg first. When the Rocket-Dan get into the mix, Jackie uses his Capture Styler to borrow the power of a nearby pokemon to stand up to them. Satoshi and Pikachu enter the fray, but they still have to contend with the attacks of Phantom's powerful high tech mecha! Suddenly, the egg starts to shine with a vivid light, and Manpahy is born! What is the mystery of the legendary treasure? What mysterious powers does Manaphy have? Can Satoshi-tachi and Jackie complete their top secret mission? The journey to reach the Water Temple Akuusha has begun!