Kobato est une jeune fille qui découvre le monde des humains aux côtés d'Ioryogi, un chien en peluche qui parle et crache des flammes. Elle est chargée d'une mission : remplir une bouteille magique de "sentiments blessés". Pour ce faire, Kobato doit acquérir la mystérieuse bouteille en se montrant capable de vivre parmi les hommes. C'est le début d'un voyage initiatique pour notre jeune héroïne, qui n'est pas au bout de ses surprises...

Kobato continue sa découverte du monde des humains, toujours accompagnée de sa bouteille magique pleine de sentiments blessés. Dans cette nouvelle aventure, la jeune fille travaille à la crèche Yomogi de Mme Sayaka lorsqu'elle apprend que la directrice a de graves problèmes d'argent et qu'elle est poursuivie par des créanciers sans scrupules. Heureusement, Kobato s'active pour aider Mme Sayaka et propose d'organiser une kermesse, avec les enfants de la crèche afin de récolter de l'argent...

Kobato's mission to fill up her magic bottle might just be on the backburner. It seems that the members of Yomogi Kindergarten's staff are no strangers to wounds of the heart, but despite Kobato's efforts, she's no closer to healing either Sayaka-sensei or the ever-solemn Fujimoto-kun! Moreover, the center is still on the verge of being shut down by unscrupulous gangster types! Leaving Kobato to her own devices, Ioryogi-san meets (read: clashes) with some odd characters from his past and uses his otherworldly connections to investigate Yomogi. Who is Ioryogi-san really?! And will Kobato's sheer determination to help those around her be enough to unravel the kindergarten's secrets and save the hearts of its staff from despair?!

Still unable to provide solace to the hearts of Sayaka-sensei and Fujimoto-san, Kobato is at a standstill in the process of healing the wounds of Yomogi Kindergarten. And so prompted, the belligerent blue Ioryogi-san, Kobato's plush mentor (read: drill sergeant), takes it upon himself to do a little digging into the school's backstory. But en route from his successful fact-finding mission, Yomogi's past turns into the least of Ioryogi-san's worries when his own past catches up with him! And with it comes a declaration: Time is running out for Ioryogi to help Kobato fulfill her quest! But as the seconds tick away, will Ioryogi-san be able to light a fire under Kobato, whose head and heart have become clouded by what seems like love...?

As the seeds of love begin to bloom in her heart, Kobato's attentions are diverted from giving solace to strangers and filling up her magic bottle in order to finally earn her mysterious wish! Now it seems all Kobato has eyes for is the dour Fujimoto-kun and putting a smile on his face. With this turn of events, Kobato is fighting to save Yomogi Kindergarten more than ever before, all at the expense of her magic bottle. But as time runs out for her quest, is Kobato unwittingly endangering her wish, her life, and the lives of Ioryogi and his erstwhile allies (read: cronies) by choosing to follow her heart?

Kobato herself has finally awakened to the feelings of love she possesses for Fujimoto. And she's more determined than ever to go to any lengths to heal his heart, even if it means breaking her own. But inside of Kobato, yet another, Iorogi's angel, begins to open her eyes as well. As their worlds collide and the deadline for Kobato's wish comes due, will she actually be able to get what she longs for without the magic bottle? And where will that wish ultimately leave her friends from both the human world and the other world?