In the distant future, because of an interplanetary war that had continued on for centuries, civilizations were ruined. Human beings have lost everything, and only 1/5th of the population survived. A strange breed of humans, ''The Third'' is said to have appeared just after the war. They possess a third eye, as their name suggests, that appear as oval-shaped red pupils called "space eyes'' over their conventional two eyes. Using them, they can control computer systems and so on, and as such, rule the world by their superior power over technology. In this world, there is a young woman named Honoka; she is a "jack-of-all-trades" sellsword, and she accepts any job except murder. One day, she happens to find and rescue a young man named Ikus in the desert. Entering his world, and accepting a job from him, the adventure begins for Honoka and Ikus.

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]

Millennia ago, a war was fought between the Netherworld and the Spirit World. Ultimately, the Netherworld was destroyed and Lord Yakumo, the King of the Netherworld, was banished to the depths of space. Now, five defenders from the Spirit World must team-up against Yakumo's Demon-Gods for possession of five, mystical sites. But Lord Yakumo is dangerously close to reclaiming the Power Sphere—the source of the Netherworld's energy—and once it is again in his possession, our world will become the new Netherworld.

Kaoru Hanabishi, a college student who lives alone, met a beautiful but bewildered girl dressed in a kimono at a train station. He volunteered to guide her way to the address she was looking for, which happened to be in his neighborhood, but turned out to be an empty lot. Not knowing what to do next, Kaoru invited the devastated girl to his apartment and asked for any additional clues to her destination. She supplied him with a photo of two children whom Kauru immediately identified as himself and Aoi Sakuraba, his childhood friend. It turned out that the girl in front of him is Aoi Sakuraba herself, his betrothed fiancee who came all the way to Tokyo to marry him. Her revelation was not only surprising but also reminded the deepest part of Kaoru's memory for why he left the Hanabishi family in the first place.