The second season of Megami no Café Terrace. The Familia Café Terrace opens once again, with rival restaurants opening right next door!

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...

Jougorou Kobato has a habit of inserting himself into other people's problems. After realizing his detective skills are neither wanted nor appreciated, he makes an agreement with his shy friend Yuki Osanai to become ordinary together. Now entering high school, they aim to be perceived as regular people, yet Kobato cannot help but fall back into his deductive ways when faced with everyday mysteries. Unfortunately, mundane occurrences are not all the duo stumbles across. As they go through their school days trying to avoid drawing attention to themselves, Kobato and Osanai at times get caught up in incidents that put their plan of a peaceful, average life at risk.

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.