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...

The night of a family birthday party. The mother is tired from work and wants to drink a beer as soon as possible. The father is fidgety and keeps an eye on the clock. A little girl is excited about the sumptuous meal and runs around the house. The intercom rings. There, a "new family member" is standing there... (Source: Official site, translated)

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Jun is a very intelligent little girl who spends her time arranging all kinds of inventions. It goes until creating two small robots, Kichinosuke and Yukinojo, who become her best friends. Because of her intelligence, Jun gets into college at a young age and she meets and falls in love with a boy from her class who's called Zero. Zero is interested in motorbikes and not in school and is accustomed to not attending the courses. He got delayed in his schooling and thus is found much older than the other students and is there for humiliated for it. On the other hand Jun is way too young and little to be in college and is made fun of. Thanks to their common passion for mechanics, Zero will sympathize with Jun and will agree to dine with her in Harbor, the restaurant where Jun's parents live. This is long series of fun adventures and arguments that little Jun will make to allure her charming prince, who's twice older than her.