As an assistant to Sinnoh's resident Pokémon Professor, Mitsumi tirelessly cycles for an errand when she witnesses a peculiar sight—a horde of Eipam joined by a boy, Hareta, wearing nothing but shorts! Having the ability to develop special bonds with Pokémon ever since he was an infant, Hareta has lived with the creatures by the forest all his life, and as a result, knows little to nothing about human society.

When Doctor Nanakamado asks him if he would like to meet a god-like Pokémon called Dialga, Hareta enthusiastically accepts, setting out on his quest with Mitsumi and the prideful Water-type Pokémon Piplup by his side. However, Hareta and Mitsumi soon learn during their Gym Badge-collecting travels that they are not the only ones who wish to meet the Legendary Temporal Pokémon. A mysterious group called Ginga-dan has been doing horrible things to both humans and Pokémon, and the mastermind behind their agenda is a fearsome leader who threatens to seize Dialga's temporal powers all for himself.