|“||The time has come. Human beings must be brought to JUSTICE!||”|
Thousands of years ago, a giant and deadly meteor was hurtling towards the planet Earth, threatening to destroy it. But all of a sudden, Arceus appeared and summoned all of its powers from its plates to destroy the meteorite and save the world. The cost of it was so high, the force of the meteor's explosion caused Arceus to lose all of its plates and crash land in the mountains. At that time, a man named Damos, who witnessed Arceus's brave and noble act found Arceus dying from its injuries and finds one of the missing plates. He returns it to Arceus. This gives Arceus the strength to pull back the other missing plates and somehow fully recover. After that, Arceus and Damos became close friends. Sometime after, Michina Town faced a terrible famine. All of the crops, trees, and plants were withered and dry. The water in the rivers was dried up, too. Damos knew that everyone would be on the brink of starvation if the land wasn't flourished. So Arceus, in deep gratitude for Damos's previous actions, decided to lend Damos his strength. He combined the Splash, Earth, Meadow, Zap, and Draco plates to create a beautiful artifact called the Jewel of Life and gave it to Damos. Arceus told him to only use it for the greater good and to make the land rich and fertile. After that, the power of the Jewel of Life flourished Michina and the land became desolate once again. Arceus then decided to wait for next solar eclipse so Damos could fulfill the promise to return the Jewel of Life. But when Arceus came to reclaim the Jewel, Damos suddenly turned against Arceus and attacked it instead, much to Arceus's shock. But Arceus somehow managed to fight off the attack and sent Damos to his impending doom. Arceus then went back to its dimension to recover from its injuries and vowed to bring all humans to justice.
Millennia later in the present day,Arceus's awakening from its long, eternal slumber causes time and space to become distorted and brought both Dialga and Palkia's dimensions, which were designed to remain eternally separated, into contact with one another. The intersection then caused Dialga and Palkia to battle against each other in Alamos Town while both of them believed that the other invaded their territory. The battle even affected the Reverse World, which caused Giratina to become involved in the conflict as well.
When Arceus finally awakened from its slumber, it returned to Michina Town and began to destroy it with its signature move, Judgment. Damos' descendant, Sheena, attempted to make things right by returning to Jewel of Life back to Arceus. Arceus then steps on the jewel, and it shatters. Arceus is furious and tells Sheena that the Jewel of Life cannot, and will not, break. The group realizes that it was a counterfeit. Arceus prepares to use Judgement to continue destroying Michina Town. Sheena pleaded it to stop by connecting with its heart, but it was jealous and Arceus continued its assault. Suddenly, Dialga, Palkia, and Giratina arrived and protected Ash and his friends from Arceus' attacks. While Giratina and Palkia holds Arceus off, Dialga sends Ash and his friends back in time to the day of Damos's betrayal of Arceus.
In the ancient past, the group learned that Damos had been hypnotized by a selfish and greedy man named Marcus, who had grown bitter and believed that if the Jewel of Life is reclaimed, Michina would return to being a wasteland again. It was also revealed that Damos isn't the bad guy as history had made him out to be and the legend of his betrayal of Arceus turned out to be a lie. Marcus, after learning about what might happen in the future, decides to change his plan and manipulates Sheena into luring Arceus into a trap. As Sheena tried to return the Jewel, she realizes to her horror that Marcus stole it from the staff and he ordered all of Damos' Pokémon to attack Arceus and poured Silver Water on it. Damos managed to reach the last bit of life in Arceus at the last minute, giving it enough strength to re-absorb the Jewel from Ash, thus saving it from death. It then saved Ash and Pikachu from the Silver Water. It also forgave Damos after seeing in his heart that he is still a good man.
But due to the damage caused by the battle and Marcus' evil plans to destroy Arceus, the temple began to collapse and fall apart. Arceus used its powers to save everyone and destroyed the armor that was controlling all of Damos' Pokémon. It then bid Ash, Damos, Sheena and all of their friends farewell and returned to its dimension. After that, Ash and his friends returned to the original timeline, only to find that the present Arceus was still upset. When Arceus was about to deliver the final blow on the creation trio, time caught up, and Ash called Arceus. It then remembered Ash's role of saving its life in the past. After that, it restored Michina back to normal and healed the creation trio. Arceus told the gang that their ancestors has dedicated their entire lives to restoring and cultivating the land. It even said that Michina was brought back to life by the efforts of Pokémon and people alike. With the past altered and the timeline changed for good, the creation trio returned to their respective dimensions and bid a fond farewell to Ash and his friends. Arceus, who is now friendly towards humans now that the past is altered, says good-bye to Ash and his friends and finally comes to understand that it is truly apart of the Pokémon world for the very first time.