Kazuhiko Nukumizu, a self-proclaimed "background character," accidentally witnessed his popular classmate Anna Yanami being rejected by her childhood friend. Since then, Kazuhiko has become involved with several loser heroines, including Anna.

In the near future, a sudden and unexplained sea rise has left much of human civilization underwater. Ikaruga Natsuki, a boy who lost his mother and his leg in an accident some years earlier, returns disillusioned from a harsh life in the big city to find his old countryside home half-swallowed by the sea. Left without a family, all he has to his name is the ship and submarine left to him by his oceanologist grandmother, and her debts. His only hope to restore the dreams for the future that he has lost is to take up an opportunity presented to him by the suspicious debt collector Catherine. They set sail to search the sunken ruins of his grandmother's laboratory in order to find a treasure rumor says she left there. But what they find is not riches or jewels; it is a strange girl lying asleep in a coffin at the bottom of the sea. Atri. Atri is a robot, but her appearance and her wealth of emotions would fool anyone into thinking she's a living, breathing human being. In gratitude for being salvaged, she makes a declaration to Natsuki: "I want to fulfill my master's final order. Until I do, I'll be your leg!" In a little town slowly being enveloped by the ocean, an unforgettable summer is about to begin for this boy and this mysterious robot girl...

High school student Taiyou Asano has been socially inept ever since his family died in a car crash. The only person he can properly interact with is his childhood friend, Mutsumi Yozakura—the head of the world's strongest family of spies. Mutsumi's eldest brother, Kyouichirou Yozakura, has been overprotective of her ever since he once rendered her severely injured. His love for Mutsumi is lethal, and Taiyou is his next target. To survive, Taiyou must marry Mutsumi and become a member of the Yozakura family. Thrown headfirst into chaos, Taiyou begins his journey to become a powerful spy in order to protect his wife and uncover the dark secrets of his past and the Yozakura family.

In the town of Kurouzu-cho, Kirie Goshima lives a fairly normal life with her family. As she walks to the train station one day to meet her boyfriend, Shuuichi Saito, she sees his father staring at a snail shell in an alley. Thinking nothing of it, she mentions the incident to Shuuichi, who says that his father has been acting weird lately. Shuuichi reveals his rising desire to leave the town with Kirie, saying that the town is infected with spirals. But his father's obsession with the shape soon proves deadly, beginning a chain of horrific and unexplainable events that causes the residents of Kurouzu-cho to spiral into madness.