Yorito Morimiya is obsessed with the sky. He particularly enjoys photographing its many different aspects—sunrises, sunsets, and clouds. During one of his early-morning trips to capture the sunrise, Yorito encounters a strange girl arguing with a vending machine. By the time Yorito manages to retrieve the girl's tomato juice from the machine, she has vanished without a trace. Sola follows the story of Yorito, his sister Aono, and their childhood friends Mana and Koyori Ishizuki, as well as that of a mysterious girl who appears and disappears, and who seems to harbor a dark secret. In a world where magic and the supernatural are never far below the surface and no one is who they seem to be, love and loneliness vie for supremacy beneath Yorito's sky.