A long time ago, the people of Camaron Palace found themselves on the brink of destruction. Fortunately, they escaped it when Sir Aaron, the True Guardian of Aura, saved them. He sacrificed himself to stop a war between kingdoms. From that day on, a tournament is held every year to commemorate his noble deed.

Satoshi, a budding Pokemon trainer from Kanto, manages to win the latest tournament and is allowed to wield a staff said to have belonged to Sir Aaron himself. Lucario, the Aura Pokemon—who is also the servant of the True Guardian—emerges from the staff. However, remembering his last memory of his master abandoning him, Lucario runs away in confusion. 

Meanwhile, Pikachu, Satoshi's companion, is abruptly taken by a Pokemon named Mew to the legendary Tree of Beginning. Only Lucario knows the way there, but he is unwilling to trust humans after his master's betrayal. Even so, to save his partner, Satoshi and his companions must acquire all the help they need and travel to the Tree of Beginning, unfolding hidden truths from centuries ago.

[Written by MAL Rewrite]

One year has passed after the great battle against the "Orochi" (gigantic snake). Tenka had been paralyzed from the final battle and he took part of the government's human experiment before the battle. Tenka withdrew himself from society, but his younger brothers, Soramaru and Chuutaro, find out the secret past about their older brother. (Source: Amazon Prime Video)

Residing within Tokyo's district of Ueno are the Colors, three individuals who protect their city by performing good deeds and aiding their community. Or, at the very least, they pretend to be the city's defenders. In reality, the Colors are just three young girls: the shy Yui Akamatsu, the noisy Sacchan, and the video game-loving Kotoha, who spend their time playing make-believe and exploring the city. The Colors' activities are facilitated by the grandfatherly Daigorou "Pops" Kujiraoka, who uses his store's inventory of knick-knacks to entertain the rambunctious trio. Not everyone is a fan of the Colors though. The local policeman Saitou just wants to deal with his regular duties, but he often finds himself the target of the Colors' attention, having been made the villain in most of their fantasies. But despite his personal feelings, Saitou always finds the time to go along with the three girls' games. Even though the Colors do not actually defend Ueno, they definitely help brighten everyone's day. [Written by MAL Rewrite]

As they continue their journey through the Johto region, Satoshi and his friends visit Altomare, an island city that hosts an annual racing event called the Pokémon Water Race. While Takeshi and Kasumi are enjoying themselves, strange things seem to be happening to Satoshi—he somehow loses the water race, sees some women attack a girl with their Pokémon, and despite them saving her, the girl later denies ever seeing Satoshi and Pikachu before!

Fortunately for Satoshi, his confusion clears up as he learns that the girl he and Pikachu saved earlier was actually a Pokémon named Latias, who likes to disguise herself as her human friend, Kanon. Latias and another Pokémon, Latios, are known as the Eon Pokémon, as they inhabit and guard Altomare along with a mystical blue sphere called the Soul Dew. An ancient legend of Altomare is highly connected to the Eon Pokémon and the Soul Dew, and is well known among the locals—as well as among Latias' earlier assailants, the thief sisters Zanner and Lyon. As the thieves attempt to capture both the Eon Pokémon and the Soul Dew, Satoshi is forced to act in order to stop them from bringing disaster to Altomare.

[Written by MAL Rewrite]