In the near future, much of the world has been forgotten at the bottom of the ocean due to rising sea levels. Natsuki Ikaruga, who lives in a small town surrounded and stranded by the sea, is invited by a mysterious woman, Catherine, to search for a treasure in his grandmother's house who was a marine geologist. One day, he dives to the bottom of the ocean in a submarine and encounters a mysterious capsule with a girl sleeping inside. The girl was a humanoid so sophisticated that she could be mistaken for a human.

"I'll be your leg, Master!" Atri, who was supposed to be with Cathrine, has come back to Natsuki. Although she was pumped to be of assistance to her new master, she fell into the ocean while carrying him and failed at cooking… It's as if she is a piece of scrap. Atri seems to have received a very important order from Nonko and tries to remember what it is, but...

Natsuki accompanies Atri who is on her way to school. However, when they arrive, they find that most of the school is underwater. Although they managed to get into the school building, inside it was full of empty classrooms and an unexpected teacher. There, Natsuki is faced with the saddening reality of the lives of the people who remained in their town.