Kyoko Byakuya feels an inexplicable attraction to the base of Mount Sengoku and discovers a unique feature there: volcanic hair with a golden hue that is rare in Japan. A strange man named Aizawa, who seems to have been expecting her, takes her to his village, Kiyokami. There, she learns about "Amagami," which is the village's ability to perceive each other's thoughts due to the golden hair. Before leaving, she is invited to a stargazing tradition; however, it quickly turns grim when a swarm of mysterious objects fills the dark sky, replacing the comforting golden hue with dark, jet-black hair.
The following day, Kyoko is found at the wreckage of Mount Sengoku with the same golden Amagami hair as the villagers. She must act quickly to prevent an unknown terror from destroying humanity and unleashing a cosmic nightmare, especially with the recent strange occurrences in the sky and the terrifying events of the stargazing ceremony.