Suzume, 17, lost her mother as a little girl. On her way to school, she meets a mysterious young man. But her curiosity unleashes a calamity that endangers the entire population of Japan, and so Suzume embarks on a journey to set things right.

Makoto's grandfather was the principal of the great Onodera Academy, and when he passed away, he left Makoto and his school staff with one very important will - "The one man who is able to seduce Makoto with his superb sexual techniques will be given the right to take over as Onodera Academy's new principal!" Because of this ridiculous last request, Makoto is now every faculty member's target for sexual harassment! Desperate to protect his virginity, Makoto seeks help from his childhood friend (and the man who he has always loved), Kintaro.

The summer of his high school freshman year, Hodaka runs away from his remote island home to Tokyo, and quickly finds himself pushed to his financial and personal limits. The weather is unusually gloomy and rainy every day, as if taking its cue from his life. After many days of solitude, he finally finds work as a freelance writer for a mysterious occult magazine. Then, one day, Hodaka meets Hina on a busy street corner. This bright and strong-willed girl possesses a strange and wonderful ability: the power to stop the rain and clear the sky.