Welcome to the Nelos region. A new uncharted region full of Pokémon from all over the world. This area has attracted attention from the other regions and a large metropolis called Academy City has been created to research Nelos' unique history. One female student has just started her Pokémon journey and meets an unfortunate boy. Index characters in the world of Pokémon.

Kamijou Touma, from A Certain Hometown, wants to be a Pokemon Master. There's only one problem... Kamijou can't catch any Pokemon! To win Pokemon Battles, he'll have to battle them himself and make alliances with cute girls who think they're Pokemon. With misfortune, a PokeStrategist and the Imagine Breaker, Kamijou dreams of becoming a Level Zero Pokemon Master!

A certain girl named Misaka Mikoto, who was living in New Bark Town, was given a task by Prof. Elm to raise a Pokemon to help him on his research. But who can ever think that this simple request can challenge her to her limits as a trainer.

Academy City has many experiments, some cuter than others.

Famous for having every Pokedex and Pokeball fall apart on him, Kamijou Touma is lost in the Viridian Forest. Chased by a swarm of Beedrills, he's saved by a cute girl... who thinks she's a Pikachu! With a certain magical Pokedex, a growing team of Pokemon girls, and a strange power in his right hand - Kamijou's journey as a Level Zero Pokemon trainer begins. (Feel free to adopt)