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)

In a world where Pokémon live and communicate with each other, there are mythical treasures known as the Time Gears that regulate the flow of time in their respective areas. If one is removed from its resting place, time will freeze in that area, so even evil Pokémon do not dare to steal them. But recently, anomalies in time have been appearing throughout the land, causing the appearance of Mystery Dungeons and violent Pokémon. Pokémon exploration teams have been formed to explore these Mystery Dungeons, arrest the violent Pokémon, and help maintain the peace. It turns out that the anomalies in time have not been caused by the recent disappearance of the Time Gears, but by Temporal Tower slowly falling apart and Dialga corrupting into Dark Dialga. The newly infamous thief Juptile had stolen the Time Gears in order to take them to Temporal Tower and stop its deterioration. The Pokémon exploration team Team Pokédans—which consists of Hikozaru and a once-human Pochama—must team up with Juptile to go to the Phantom Land where Temporal Tower is located. If the trio fails, Temporal Tower will completely collapse, leaving the whole world frozen in time forever...

Kenta, a Pokemon master in the making, meets up with his childhood friend, Marina, at a Pokemon Center, to see how their skills have developed. Their battle is interrupted by a thunderstorm and the arrival of Bashou and Buson, two Roketto-Dan members using the Crystal System (which attracts Electric-type Pokemon). Their ultimate goal is to, under the guidance of Shiranui-hakase, bring Pokemon back to Sakaki. Kenta and Marina stumble upon this plan, and they try to stop it, but things get more difficult when the legendary Pokemon Raikou is captured. (Source: ANN)

By embracing challenges, learning from failures, overcoming obstacles, and beating the best in the world, Satoshi finally achieves his long-held dream. His adventurous spirit, however, still runs high as he continues to explore new regions, witness unfamiliar Pokémon, and forge unexpected friendships and rivalries. As the world opens its vast horizons to Satoshi, he once more encounters the people who helped shape his momentous path to success. A legendary journey nears its end just as an entirely new one is about to begin, with the bond between humans and Pokémon continuing forevermore.