red]Set in the middle of summer, Air's story revolves around three girls whose lives are connected to the same man. Yukito Kunisaki, the main protagonist, is a showman traveling across Japan, continuing his mother's search for the "girl in the sky".

At the beginning of the story, Yukito comes across a small seaside town where the story takes place. On his first day in town, Yukito tries to earn money by putting on a mysterious puppet show for kids he finds by manipulating a doll magically without strings. Yukito is unsuccessful in gaining the children's favor, and the children end up running off without paying him for his performance.

Defeated after not getting any money, and not having enough for even a meal, Yukito falls asleep on a seawall near the beach. He awakens the next day to find beside him a young girl who introduces herself as Misuzu Kamio – a sincere yet clumsy girl who is eager to become friends with him. Misuzu persistently attempts to play with him, while Yukito tries to refuse her efforts. When Misuzu finds out Yukito has not eaten anything since the day before, she suggests that he come to her house and eat for the time being. Lured by a chance to eat, Yukito follows her back home. Upon learning of Yukito's lack of lodging, Misuzu suggests that he stay at her home until he can find a place in town while he earns money, despite Yukito's hesitance to go along with her plan. That night, Haruko – Misuzu's aunt and foster-mother – comes home and after Yukito and Misuzu persuade her, it is decided that he will stay with them on two conditions: that he sleeps in the shed, and that he shares a drink with Haruko
As Yukito resides with Misuzu, he meets two other girls, Kano Kirishima and Minagi Tohno, who like Misuzu, have strange personalities connected with mysterious pasts. Before long, a legend of "one thousand summers" begins to unfold where the mysteries of the past are framed by the odd relationship between Yukito and Misuzu