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)

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]

In ages long forgotten, when Earth found itself on a collision course with a meteor, Legendary Pokémon Arceus used its power to avert the danger. However, this feat caused the 16 Plates surrounding it to scatter across the world. Without the Plates providing Arceus with life energy, it began to die. A human named Damon managed to find one of the Plates and returned it to the moribund Pokémon, helping it recover. As a reward, Arceus created the Jewel of Life and gave it to the people of Michina Town, stipulating that it must be returned, but the humans refused, hogging the Jewel to themselves. In the battle that ensued, Damon was killed and Arceus went into slumber, vowing to punish humanity upon its return.

Satoshi and his companions arrive in Michina Town where they come across Sheena, a descendant of Damon, who claims to be in possession of the Jewel of Life and intends on giving it back to Arceus when it awakens.

The situation takes an unexpected turn when Arceus, despite Sheena's best intentions, remains unsatisfied. Satoshi must now prevent the destruction of the entire human race, as Arceus' fury causes distortions in the fabric of the universe, enraging the Legendary trio—Dialga, Palkia, and Giratina—and disturbing the world's balance.

[Written by MAL Rewrite]

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.

[Written by MAL Rewrite]