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.