The game shifts away from standard Kanto storylines to deliver a mystery-driven campaign. Players step into the shoes of Colin, whose father, Ethan, presents him and his best friend, Nate, with their very first partner Pokémon. On the same day, Ethan unveils a groundbreaking invention developed in collaboration with his close friend, Mael. However, the celebratory atmosphere is shattered when Nate's brother, Kyle, suddenly disappears, and soon after, Ethan goes missing as well.