One day, Red, a boy filled with dreams of going on a Pokemon journey, is called to Professor Ookido's lab. There, Professor gives him and his rival Green a Pokedex in order to collect data on all of the Pokemon in the region. As Red works his way to become champion with his Hitokage, he meets many people on his journey, including Fuji Roujin, a man who runs the home for abandoned Pokemon, and Reina, a girl who works there. As danger in Red's journey begins to peak, he and his partner Pokemon experience a transformation like never before.

Source: ANN

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Same setting: Pocket Monsters