In June 2021, a young high school student named Hodaka Morishima finds himself running away from home, seeking a fresh start in Tokyo. His journey begins with a perilous encounter during a heavy rainstorm when his ferry is caught in a torrential downpour, almost sweeping him away. Fortunately, he is saved by Keisuke Suga, who provides him with a business card and advises him to call if he needs work. Despite this, Hodaka struggles to find stable employment in the busy city, but his situation takes an unexpected turn when he discovers an abandoned Makarov PM handgun—an illegal weapon that he keeps for protection, even though guns are outlawed.
During his search for help, Hodaka crosses paths with Hina Amano, a compassionate young woman working at a McDonald's. She quickly shows empathy for his situation and offers him free food, which becomes a small act of kindness amid his struggles. Soon after, Suga hires Hodaka to assist him in putting together a small occult magazine that investigates strange phenomena, including the unpredictable weather patterns plaguing Tokyo. As they dig into local legends, they come across the story of "sunshine girls" who have the mysterious power to clear the skies and bring sunshine on demand.
Hodaka witnesses a distressing scene where Hina is being coerced into working at a club. In a panic, he fires his gun at the club owner, narrowly missing him, which leaves Hodaka shaken and frightened. To protect himself, Hodaka throws the gun away. Hina then takes Hodaka to an abandoned building called Yoyogi Kaikan, where they find a shrine on the roof. To his amazement, she demonstrates her unusual ability by praying and clearing the sky of clouds, revealing her remarkable power to control the weather through prayer.
Hina, an orphan living alone with her younger brother Nagi, has been trying to keep their lives afloat amid their financial struggles. Observing her hardships, Hodaka proposes a bold idea: they could start a business offering to clear the weather for social events, weddings, and outdoor gatherings. Their venture quickly becomes popular, bringing in more requests than they can handle. However, as Hina's fame grows, she is filmed for television, which results in their website being flooded with requests. Recognizing her need for rest, they decide to temporarily pause their operation.
Meanwhile, Suga and Natsumi are investigating the phenomena further. They interview an old shrine priest who shares the legend of "Weather Maidens"—women who possess the extraordinary ability to manipulate rain. The priest warns that such powers come with a heavy toll, hinting at the potential sacrifice involved.
Amid their crises, police begin to search for Hodaka, who has been reported missing by his family. Law enforcement officials track him via security footage of him using the illegal gun. They eventually locate Hina’s apartment and interrogate her, realizing that without a legal guardian, she and Nagi could be taken away by social services. Suga, who is also visited by the police, makes the difficult decision to fire Hodaka, explaining that the authorities suspect him of kidnapping. He gives Hodaka a sum of severance pay before he leaves.
Feeling cornered, Hodaka, Hina, and Nagi decide to run away together, as relentless, unnatural weather—ranging from continuous rain to snow—closes in on Tokyo. The city declares a state of emergency due to the severe and abnormal climate chaos. Hodaka is eventually caught by the police, but Hina intervenes, unintentionally using her powers to destroy a police van with lightning to save him. They find shelter in a hotel using the cash Hodaka has received from Suga, where Hina confesses that her body is gradually turning transparent with each use of her power—a sacrifice she makes to bring normal weather back to the city.
The next morning, Hina has disappeared, and the relentless rain has stopped. The police catch up with Hodaka at the hotel, and he is taken into custody. Nagi is placed into a children’s counseling center as Hina’s presence becomes a distant memory. Overcome with the realization that he loves Hina, Hodaka escapes from custody with help from Natsumi, Suga’s niece. In a daring rescue, he is saved from apprehension by Suga himself, who, inspired by Hodaka’s determination, helps him break free.
Hodaka then ventures to the rooftop shrine where he finds Hina praying. He begs her to return with him, urging her to let go of her worries about the weather and start living for herself. As Hodaka pleads, Hina joins him, and together they step through the torii gate into the sky, symbolizing hope and possibility. However, their reunion is short-lived—once back at the shrine, all five are arrested, and the heavy rains resume, flooding much of Tokyo.
Hodaka is sentenced to a three-year probation and sent back to his home on Kōzu-shima. Years pass, and Tokyo continues to be submerged under endless rains, with much of the city beneath water. It’s now spring 2024, and Hodaka, having completed his probation, graduates from high school and returns to Tokyo to attend college. He reconnects with Suga, who has now expanded his weather-related business, and is encouraged to find Hina once again. Eventually, Hodaka spots her praying on a street overlooking the drowned city. They reunite, and Hodaka promises her that everything will be alright, rekindling hope for their future together amid the flooded landscape that once kept them apart.
