U.C. 0097, one year after the opening of "Laplace's Box". Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix… named Phenex.
Ash, Pikachu, and their friends come to a desert city by the sea. Here they meet the Mythical Pokémon Hoopa, which has the ability to summon things—including people and Pokémon—through its magic rings. After a scary incident, they learn of a story about a brave hero who stopped the rampage of a terrifying Pokémon long ago. Now, the threat that has been bottled up for years is in danger of breaking loose again.
In the underground Diamond Domain, where many Carbink live, the Mythical Pokémon Diancie serves as ruler. The Heart Diamond that sustains the land is beginning to fall apart, and Diancie is not yet strong enough to create a new one. While seeking help from the Legendary Pokémon Xerneas, Diancie encounters a group of thieves who want to take control of its diamond-producing power–and who awaken the Legendary Pokémon Yveltal from its cocoon in the process! Can Ash and his friends help Diancie discover its true power, stop Yveltal’s rampage, and save the Diamond Domain?
In the spring, male student Makoto Yuki transfers to Gekkoukan High School. However, as he heads to his new dormitory, listening to the music on his headphones, he is stopped. More precisely, time has stopped, and the people who were around him turn into coffins. Makoto learns that this period of time hidden between the minute of midnight is called the Dark Hour, a time when monsters called Shadows appear. Suddenly made the leader of his fellow classmates Yukari and Junpei by his upperclassmen Mitsuru and Akihiko, Makoto must learn empathy, his connection to his comrades, and the meaning of death. With the power of his Evoker aimed at his head, Makoto fights against the Shadows threatening to attack his world from the mysterious tower of Tartarus.
While sorting through a mess of books in the staff room, Ohana happens upon one of Denroku's log books from long ago. Within it, it recounts a story of Ohana's mom when she was the same age as her.