The story begins with the player riding in a moving van with Professor Baro (who replaces Professor Birch's role in Pokémon Ruby, Sapphire, and Emerald Versions). The player and his mother have just moved in to Breeze Town of the Corna region, which is a heavily modified Hoenn region. Coincidentially, the player's rival and his/her mother have moved in to the next-door house around the same time. Upon meeting the rival, he/she immediately develops a crush on the player while doing a poor job at hiding it.

The player later encounters Professor Baro at "BREEZE WY," where he is being chased by a wild Sever (Poochyena clone). Professor Baro asks the player to take a Poké Ball out of his bag, where the player may choose his/her starter Pokémon. After choosing, the player battles and defeats the Sever. After rescuing Baro, he lets the player keep the chosen Pokémon as thanks for saving him. He asks the player to meet up with his/her rival at "ROCK CN." After the player battles and defeats the rival at "ROCK CN," they return to Baro's lab, where they each receive a Pokédex and some Poké Balls. From there, the player may travel to more cities and towns, battle and defeat the Gym Leaders of the Corna region, and challenge the Pokémon League. Along the way, he/she will encounter Band Ambar, an electric-based evil organization led by Amber whose goal is to "inflate the sun" to make Electric-type Pokémon more powerful.