Kobato Hanato is the protagonist of the story, a mysterious young woman who arrives on Earth with a mission to heal the hearts of suffering people. By easing their emotional pain, she collects crystallized fragments of healed hearts, which take the form of konpeito candies, into a magical bottle. If she succeeds in filling the bottle before four seasons pass, her wish to go to a specific, cherished place will be granted. Her origins are enigmatic; she is a wandering soul from another dimension existing in a liminal state between life and death. She has no memories of her past and is never seen without her hat, which hides a crown that signifies her spiritual nature.

Her personality is marked by a cheerful and enthusiastic outlook, matched by a deep innocence and a sincere drive to help others. She is unusually dedicated but also remarkably clumsy and naive, often lacking common sense about the human world and tripping over her own feet. The primary motivation driving her actions is the desperate desire to fill her bottle to reach the place she longs for. A strict rule of her mission forbids her from falling in love with anyone whose heart she heals, establishing a central internal conflict.

In the story, Kobato takes on the role of an assistant at the Yomogi Nursery, a struggling daycare center run by Sayaka Okiura, which grounds her in everyday human life. Her most important relationship is with Ioryogi, a powerful spirit from the Spirit Realm forced into the form of a blue plush dog. He acts as her guardian, mentor, and critic, grading her progress daily while harboring a deep, protective care for her. She also develops a profound bond with Kiyokazu Fujimoto, a cynical law student who works at the nursery. Despite his initial harshness, he grows to love her, and reciprocating those feelings forces Kobato to directly confront the limits placed upon her.

Kobato’s notable abilities are tied directly to her empathic nature. She is a beautiful singer, often using her voice to calm and heal those in distress. Her primary power is the absorption and crystallization of others' suffering into the bottle. Throughout her journey, she undergoes considerable development, transitioning from a bumbling outsider into a vital member of the community. As she gradually recovers fragments of her lost memories, she uncovers the truth about her own tragic past and the connection between her soul and Ioryogi, ultimately facing a pivotal choice between achieving her wish and embracing the love and life she has found.