Kobato Hanato is a girl with a mission: fill up a mysterious bottle she carries with her all the time. There's a place Kobato wants to go, and she can only go there once the bottle is completely full. In order to fill her bottle, she needs to find people with sorrow and heal their hearts. The more she heals, the more her bottle fills itself.
However, Kobato is not so sure of how to make it and where to start, so she moves to an apartment complex to search for those people and start her mission, along with her little mascot, Ioryogi, a little blue dog who seems very cute but can also be terrible rude and scary every time Kobato does something stupid.
Later on, Kobato meets Sayaka Okiura, a teacher from the local nursery school who seems to be needing some help with the school's duties. Thinking that she might be healing her wounded heart, Kobato offers herself to assist the teacher in what she needs. But only helping Sayaka at the school might not mean the end of her suffering, and Kobato needs to realize how to do it.
Kiyokazu Fujimoto also works at the school, and he seems to know Sayaka ever since his childhood so he really cares about her. Because of that, he tends to not trust so easily in the people that approach Sayaka, fearing that they might want to abuse of her kindness, as many times before. To make sure Kobato isn't one of them, he'll keep an eye on her intentions and make sure she's not trying to take advantage of Sayaka.
In the meantime, Kobato must proove to him that she's there to help the biggest number of people while realizing that Fujimoto might as well have a wounded heart too.
Kobato will try her best to fill the bottle as soon as possible so that she can grant her wish and go to the place she wants to go.