Jun Shirasaki and the Jinguuji sisters are childhood friends and neighbors. When Jun's first girlfriend, the older sister Ryuumi, breaks up with him, she says something that complicates the three people's relationship, their first loves, and their romance—?

Makoto Hanaoka, a womanly second-year student, easily attracts other people's attention. First-year student Saki Aoi is no exception, and she falls in love with Makoto at first sight. Having a vibrant and vigorous personality, she does not hesitate to confess her feelings to her senior. However, Makoto differs significantly from the person Saki perceives: Makoto is not a girl, but rather a cross-dressing boy! After revealing his well-known secret to Saki, Makoto expects her to be disgusted. Surprisingly, she is instead captivated by this revelation. Nonetheless, he still rejects her, but Saki's determination does not stop her from declaring that she will become his first love. With Saki and his childhood friend at his side, Makoto's world brightens, giving him strength amid his struggle between his interests and the expectations placed on him.

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...