In a certain city in Japan, one's heart faintly shimmers above the rest—a seemingly odd and naive brunette named Kobato Hanato. Despite appearing to wander around, the pure-hearted girl aspires to fulfill one precious wish: to reach a particular place. But for it to be granted, she must learn how to heal the wounded hearts of the people and collect them in a magic bottle.

However, the world can be confusing for such an innocent girl. Her companion Ioryogi can be quite rough in teaching her common sense, especially for a talking blue dog plushie! Luckily for Kobato, a certain quaint place with a troubled history seems to be—and may be looking for—a glimmer of hope.