Five years ago, gravity-defying bubbles with mysterious powers rained down upon the earth. After a huge explosion of uncertain origin, Tokyo became ground zero, with the city being enclosed in a gigantic bubble. As a result of this "Bubble Fall" phenomenon, the metropolis that was once the capital of Japan drowned in a gravity-bending sea; the government declared it a prohibited zone, and the residents abandoned it. Children orphaned by the Bubble Fall now squat illegally in Tokyo, partaking in dangerous parkour team battles across the city's dilapidated buildings. Hibiki—a talented ace in these games with the ability to jump between bubbles—claims he can hear sounds from the Tokyo Tower. Determined to uncover its mysteries, he sets off toward the source, but he falls into the waters below. A strange girl, whom he later nicknames Uta, saves him. But little does Hibiki know that Uta's appearance in his life will reveal the secrets behind the disastrous event that changed their world forever.

Tokyo is currently experiencing rain showers that seem to disrupt the usual pace of everyone living there to no end. Amidst this seemingly eternal downpour arrives the runaway high school student Hodaka Morishima, who struggles to financially support himself—ending up with a job at a small-time publisher. At the same time, the orphaned Hina Amano also strives to find work to sustain herself and her younger brother. Both fates intertwine when Hodaka attempts to rescue Hina from shady men, deciding to run away together. Subsequently, Hodaka discovers that Hina has a strange yet astounding power: the ability to call out the sun whenever she prays for it. With Tokyo's unusual weather in mind, Hodaka sees the potential of this ability. He suggests that Hina should become a "sunshine girl"—someone who will clear the sky for people when they need it the most. Things begin looking up for them at first. However, it is common knowledge that power always comes with a hefty price...

High school student Aoi Aioi lives with her elder sister, Akane, after a tragic accident took their parents away 13 years ago. Because Akane has since been taking care of her single-handedly, Aoi wants to move to Tokyo after her graduation to relieve her sister's burden and pursue a musical career, inspired by Akane's ex-boyfriend Shinnosuke "Shinno" Kanamuro. Shinno was part of a band until he left for Tokyo to become a professional guitarist after the sisters' parents passed away, and he was never to be seen again. One afternoon, while Aoi practices her bass in a guest house, she gets startled by the 18-year-old version of Shinno from 13 years ago! As if by coincidence, the current 31-year-old Shinno also returns to the town, but he has changed drastically. There are now two Shinno's in existence, but why is the Shinno from the past present? Sora no Aosa wo Shiru Hito yo revolves around these four individuals as they confront their inner feelings toward each other and make decisions that will affect their lives from here on out.

On her way to school one day, Suzume Iwato stumbles upon Souta Munakata, a young man searching for abandoned areas. The high school girl directs Souta to a nearby ruin, but out of pure curiosity, she herself decides to head to the same destination. Once there, Suzume discovers an isolated door with a dreamlike universe lying beyond it—a place that she can see and feel, but not enter. A strange stone rests on the ground nearby, but it turns into a cat-like creature and scurries away when Suzume lifts it. Suddenly afraid, she heads back toward her school, not realizing that her act of leaving the door open will have consequences. With the "keystone" released, the evil within the other universe can now freely escape and wreak havoc throughout Japan. Intending to correct her dangerous mistake, Suzume joins Souta—whose true goal is to prevent evil from festering—in finding and locking all open doors before the country is destroyed.