Kobato is a sweet and perky girl, but also extremely naive about the world around her. She has a "mission" to fill her mysterious bottle with people's hearts she heals so her wish to go a certain place can be granted. However, the restriction is that she is not allowed to fall in love with any person whose heart she heals.
As Kobato attempts to fulfill her mission, she is accompanied by Ioryogi, a spirit in the form of a dog plushie. Because Ioryogi is responsible for a punishment that has been applied to him and is friends from the spiritual world, he must guide Kobato and ensure that she succeeds her mission so he and his friends might return to their true form.