On the sky island of Onobori, a village built on a celestial island where long banners flutter in the wind to protect inhabitants from fatal falls, four-year-old Aka lives with her grandfather Gino in a cozy café renovated from a windmill. Her days are filled with exploration until she befriends a mysterious giant black cat named Noirou. Into this enchanted hamlet arrives Nodoka Daidai on a flying scooter, a young woman assigned as a Guardian of the Young Leaves with a mission to watch over Aka, ensuring her happiness and growth in a world where children are rare and precious. As Nodoka, who is barely an adult herself and initially inexperienced, observes with concern Aka braving the dangers of the labyrinthine alleys and steep staircases alone, she discovers a community where everyday moments are imbued with magic and wonder. The narrative follows Aka as she explores her surroundings, shares meals with the giant cat who might be a local deity, and encounters other children in the village, including a girl named Uran of ferocious visage who does not immediately welcome friendship.

The story shares its setting with Aria, taking place on a terraformed Mars, with Onobori as an island in the sky rather than in the sea. As the series progresses, a notable narrative arc involves Aka, Uran, and another girl named Verdi preparing to board at an elementary school in Neo-Venezia. This transition requires Aka to understand the implications of leaving her grandfather behind on Onobori, though Nodoka becomes a dormitory supervisor to ease the separation, and Aka must learn to overcome her sadness in her new environment.