Kobato.

Kobato Hanato, a strange and naive girl with a kind heart, arrives in the Human World and takes on several tests given by the spirit Ioryogi in order to prove herself worthy of the bottle. Due to her naïveté, Kobato gets herself into trouble until a stranger saves her.

Ioryogi tells Kobato she must heal people's heart in order to fill her bottle. She runs into a man giving out tissues and helps him by taking the whole box. While passing them out, she walks into the same stranger from before. Kobato follows him to say thank you, and ends up at a daycare, Yomogi Nursery, run by Sayaka Okiura.

Sayaka spots Kobato sleeping in a park and takes her to a friend, Chitose Mihara, who gives her a room in her apartment building. Kobato runs into a school girl, Mutsumi, outside. The next day, after failing to help anyone, Kobato gets her umbrella stolen and runs into Mutsumi again, who lets Kobato borrow her umbrella.

Kobato meets a sad looking angel Kohaku in the streets. She sees her again the next day with the doctor (Shūichirō Kudō) Kohaku loves. After talking to Kohaku, Kobato is determined to make Kohaku and the doctor go on a date. Kobato enters a lottery to get two amusement park tickets, but ends up with a crocodile doll. She bumps into Fujimoto, who gives her his tickets for the stuffed animal.

While trying to read a firefly picture book to the children at the nursery, Kobato meets the author of the book. The author asks her to not read it to the children anymore. Wondering about his strange, sad request, Kobato decides to try and find a way to cheer him up, and in the process gains another konpeito to fill her bottle, and a step closer to her wish.

Kobato receives a phone call threatening to close down Yomogi Kindergarten.

Kobato finds that Fujimoto left a report at the nursery. While ends up going to look for him at the university to try and return the report in time. There she runs into one of Fujimoto's friends, Takashi Dōmoto. Dōmoto is a young man who is always prone to offering help to others and is often worried about Fujimoto's anti-social behavior.

Kobato finds a stray kitten and takes it home with her to Chitose's apartment. However, Chitose's twin daughters, Chiho and Chise say that their mother does not allow pets in the apartment. Together, the three of them look for an owner for the cat, but the search for a home for the cat begins to remind the two sisters just how lonely they feel. Kobato decides to cheer them up with a song.

It's summer vacation for Yomogi Kindergarten and with the nursery close and no where to spend her days, Kobato continues to search for hearts to heal. Kobato sets out to find the girl that has the summer festival leaflet and comes across a falling out amongst two friends.

Kobato keeps spending more and more time at Yomogi Nursery. One day she decides to make herself useful by going to the kindergarten to help air out the futons. On the way there, she nearly crashes into Fujimoto, who is in a bad mood and criticizes Kobato yet again. Kobato learns more about Fujimoto's childhood through Miss Sayaka, who is Fujimoto's boss and runs the daycare.

Yomogi Nursery is having financial problems and is struggling to repay debts on time. So Kobato decides to help out by working part-time at Tirol Confectionery. There, she ends up playing detective when she and co-worker Yumi see that their employer Hiroyasu in poor spirits.

Kobato, a human girl, and her spirit dog guardian, Ioryogi, got to a park where they run into an old acquaintance of Ioryogi's, Ginsei. Ginsei causes trouble by stealing Kobato's special bottle that was entrusted to her by Ioryogi. This causes a fight between Ginsei and Ioryogi, as more about the nature of the bottle and Kobato's mysterious quest to heal hearts and collect them is revealed.

Fall comes and Kobato and Ioryogi spot a giant Ginkgo tree. While collecting fallen leaves from the tree with the children, Kobato learns that it is to be torn down.

Kobato and Fujimoto take the children to pick potatoes. They see a boy stealing some. After tracking him down, they find that he ran away from his home because of his grandfather's yelling.

Sayaka falls ill. Kobato calls in Shūichirō since he is a doctor. Kobato and Fujimoto aid her recovery.

The timeline for the nursery to pay their debts is running out and Kobato convinces the children to hold a bazaar in order to raise funds to prevent it from being closed. Later, Kobato meets face to face with Kazuto Okiura.

While advertising for the bazaar, Kobato finds a worn down Ioryogi who was struggling to protect his precious box of baumkuchen from harm.

Winter arrives and Kobato is warned by Ioryogi that she must accomplish her mission by spring. Meanwhile, one of Kazuto's thugs (a debt collector) hangs at the nursery's door, intimidating the children's parents. However, when he collapses on the ground, Kobato must rush him to a hospital along with Domoto. Kobato hears a confession from Domoto that she misunderstands.

Christmas is approaching, but Fujimoto has been treating Kobato coldly, making her feel certain that he despises her. Fujimoto is busy preparing his Santa Claus outfit that he wears every Christmas. Chitose tells Kobato a story about Fujimoto's mother, who disappeared one Christmas night. Domoto walks home with Kobato.

With Valentine's Day coming up, Kobato wants to throw a party at the nursery, and decides to work at Tirol again to pay for it. After work, she sees a flash and hears some voices, one of them much like Ioryogi's. They turn out to be world-jumping travelers Syaoran, Fai, Kurogane and Mokona, who she lets stay in her room until they have to leave again. They work to pay her back.

Kazuto Okiura shows up again, demanding payment. Kobato is worried, and decides to wait outside his office. When he comes out she asks him about his feelings for Sayaka and he softens. Kobato passes out from the cold rain, and Kazuto carries her back to the nursery, where Sayaka and Kazuto resolve the tension.

The nursery is torn down, leaving Kobato in despair, but she still has to achieve her goal. She wants to help Fujimoto, but she doesn't have time because she is busy cleaning the kindergarten with Sayaka. He walks away from her, thinking she was only pitying him. Her heart hurts but she doesn't know why.

In the penultimate episode of the season, Kobato's time for her mission is up, but the bottle is not full. She says goodbye to everyone except Fujimoto. However, he finds her in the park. When Fujimoto hears the truth about Kobato, that she is in fact a liminal being, he wants her to stay, and a konpeito from him fills the bottle.

After Kobato leaves, everyone forgets about her. Fujimoto suddenly remembers Kobato after seeing her konpeito, and rushes around asking people if they remember Kobato. All of them don't until he asks Kohaku. She assures him about Kobato, and that they will surely meet again. That is a several year time-skip. Fujimoto becomes a lawyer.