Satoshi and his friends travel to LaRousse, where they meet a boy named Tooi who is afraid of Pokemon due to an incident that happened four years earlier. Meanwhile, Deoxys, a Pokemon from space, has reappeared, putting a barrier around the city and kidnapping people. Rayquaza, a Pokemon that lives in the atmosphere, comes to fight it.

(Source: ANN)

A long time ago, the people of Camaron Palace found themselves on the brink of destruction. Fortunately, they escaped it when Sir Aaron, the True Guardian of Aura, saved them. He sacrificed himself to stop a war between kingdoms. From that day on, a tournament is held every year to commemorate his noble deed.

Satoshi, a budding Pokemon trainer from Kanto, manages to win the latest tournament and is allowed to wield a staff said to have belonged to Sir Aaron himself. Lucario, the Aura Pokemon—who is also the servant of the True Guardian—emerges from the staff. However, remembering his last memory of his master abandoning him, Lucario runs away in confusion. 

Meanwhile, Pikachu, Satoshi's companion, is abruptly taken by a Pokemon named Mew to the legendary Tree of Beginning. Only Lucario knows the way there, but he is unwilling to trust humans after his master's betrayal. Even so, to save his partner, Satoshi and his companions must acquire all the help they need and travel to the Tree of Beginning, unfolding hidden truths from centuries ago.

[Written by MAL Rewrite]

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!

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?

[Written by MAL Rewrite]