Pokémon are marvelous creatures that come in a variety of types and sizes, with abilities, powers, and personalities as diverse as they are numerous. Doctor Yukinari Ookido has dedicated his life to studying these fascinating beings, that can be caught, trained, traded, and battled against each other. There's only so much he can do from his lab though. With this in mind, Ookido entrusts two young boys with a Pokémon of their own and a computerized encyclopedia to catalog them. One of them, Green, is brash, passionate, slightly arrogant, and Doctor Ookido's own nephew. The other boy, Red, is equally passionate, and filled with a wide-eyed, mildly naive sense of wonder. Pokémon: The Origin follows Red in his journey through the region of Kanto in his attempt to complete his "Pokédex" by capturing and cataloging all the Pokémon that exist. Along the way he'll discover there's more to himself and his goals than he originally thought. Red will have to put both himself and his Pokémon to the test in special Gyms whose leaders are steps along the way to the Pokémon League, in order to challenge the Elite Four and become a Pokémon League Champion. Aside from his goals to become a Champion, Red has other problems brewing. There are others who capture and train Pokémon for more sinister reasons, with the infamous criminal organization Team Rocket being one of them. If Red can defeat them, fellow trainers, his rival Green, and wild Pokémon all through Kanto, he just may fulfill his own dream, and Doctor Ookido's as well.

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]

Satoshi and his friends travel to LaRousse, where they meet a boy named Tooi who is afraid of Pokemon due to an incident that happened four years earlier. Meanwhile, Deoxys, a Pokemon from space, has reappeared, putting a barrier around the city and kidnapping people. Rayquaza, a Pokemon that lives in the atmosphere, comes to fight it. (Source: ANN)

After their encounter with Team Plasma, Satoshi, Iris and Dent start a new journey in the Decolora Islands.