Hodaka Morishima is a first-year high school student who lives in a detached island located in Japan. Growing bored with his lifestyle in the remote area of his native village, he decides to move to Tokyo. However, he finds himself living his life as a NEET against the high living cost in Tokyo, and soon becomes broke and falls into isolation, also known as "hikikomori (引きこもり)." However, he finally manages to get a job as a writer in a shady & small Monthly Paranormal Occult Editorial.

After becoming a journalist, Hodaka is sent in a task to investigate the irregular weather in Japan. One day, in a corner of the crowded and busy Tokyo metropolitan, Hodaka meets a young bright and strong-willed girl named Hina Amano, who can manipulate the weather through her prayer, and then begins exploring the undiscovered truth of the world with her.