Best friends Yuu, Haru, and Kotona enjoy a tranquil high school life together. One day, however, a suspicious man pursues and stabs Kotona—a catastrophe that Yuu and Haru fail to prevent. While hastily carrying the girl to the hospital, the two boys are nearly hit by a truck but miraculously remain unharmed. Instead, they find themselves in a fairy-tale-like kingdom with an exotic diversity of people and wonderful creatures.

To their surprise, the boys discover that Yuu, who has been confined to a wheelchair since childhood, can now walk! Yet they have no time to ponder the puzzling situation, as their friend is gone. Setting off to find Kotona, Yuu and Haru stop at a local pub to inquire about her. But upon inspecting a picture of Asha, the kingdom's princess, the two have a shocking revelation.

Narrating an extraordinary adventure in a magical world, Ni no Kuni demonstrates the special connection between two separate yet parallel worlds and its manifestation of the bonds between individuals.