In June 2021, first year high schooler Hodaka Morishima escapes Kōzu-shima in order to get away from his troubled home life to Tokyo. When his ferry to the city is hit by a rainstorm, he is saved by Keisuke Suga, who gives Hodaka his business card. As Hodaka becomes broke and struggles to find work, he meets Hina Amano, an employee of a McDonald’s restaurant. She takes pity on him and gives him food. Later on, Hodaka finds an abandoned handgun in a waste bin he fell onto. After arriving at Suga’s business location, he meets him there and his niece, Natsumi. Suga hires him as his assistant at a small occult magazine publishing company, where they investigate urban legends related to the unusually rainy weather in Tokyo. From a psychic, they hear the legend of a “sunshine girl” who can control the weather.
Hodaka sees Hina being intimidated into working at a back-alley club. After a brief chase, he scares off the club owners by firing his gun into the air, thinking it was a toy. He and Hina escape; she takes him to Yoyogi Kaikan, an abandoned building with a shrine on the roof, where he throws the gun away. Hina astonishes Hodaka by demonstrating her ability to clear the sky by praying. Hodaka finds out that Hina lives alone with her brother Nagi, and they have no adult guardian. Seeing how they are in a financial trouble, Hodaka proposes to start a business with Hina with the ability of sunshine girl: a job to clear the weather for events such as weddings and parties. They create a website to accept orders and their business quickly becomes a success. However, when clearing the sky for the Jingu Fireworks Festival, Hina is shown on television and their site gets flooded with requests, so they decide to close their business.
A detective with the police search for Hodaka, as his family filed a missing person report. They find out that Hodaka was caught using the gun on a security camera. Officers arrive at the apartment where Hina lives with Nagi and interrogate her while Hodaka hides; Hina realizes that because they have no legal guardians, with their mother having died recently, social services are going to take them into custody and separate them. Right after the police leave, Suga visits Hodaka, having also been visited by the police. Suga fires Hodaka and gives him his separation pay, explaining that the police suspect him of kidnapping Hodaka. Hodaka, Hina and Nagi try to run away, but they are halted by the worsening weather. They take shelter in a hotel, and spend the night with instant food and doing karaoke. As midnight passes, Hina reveals that her body is slowly turning into water the more she uses her power. She explains that she is the cause of the abnormal weather and is intended to be a human sacrifice, and her disappearance will return the weather to normal. Hodaka promises to protect her, but the next morning, Hina has vanished into the sky and the rain has stopped.
In the morning, the police track Hodaka to the hotel room. Nagi is sent to the children’s counseling center and Hodaka is taken to the police station. Having already fallen in love with Hina, Hodaka decides to bring her back to Earth and escapes from the police custody with the help of Natsumi and her Honda Super Cub. After her motorcycle is immobilized, Hodaka resumes on-foot to Yoyogi Kaikan building to reach the shrine. Inside, he encounters Suga, who attempts to stop him. The police surround Hodaka, but Suga, now inspired by Hodaka’s desperation to see Hina, helps him escape. At the roof-top shrine, Hodaka jumps through the shrine gate and is transported into the sky, where he finds Hina and asks her to leave with him, insisting that Hina let go of her worries about the weather and start living for herself. As soon as they come back to the rooftop shrine, Hina, Hodaka, Natsumi, Nagi, and Suga are all arrested, and the heavy rains resume. Hodaka is sentenced to a three-year probation and sent back to his home in Kōzu-shima.
Three years later, the rain has been falling without end in Tokyo, submerging much of the city. In the spring of 2024, having finished his probation, Hodaka graduates from high school and returns to Tokyo to start college. He meets with Suga, who has expanded his business. After Suga encourages him to find Hina, Hodaka finds her praying on a street overlooking the drowned city. They reunite, with Hodaka promising her that they will be alright.