In a near future, an unexplained and catastrophic sea level rise has submerged much of the world's landmass, forcing humanity to adapt to a diminished existence. The protagonist, Natsuki Ikaruga, is a young man who has lost both his mother and his right leg in a tragic accident. Disillusioned with his life in the city, he returns to the coastal hometown of his late grandmother, a renowned oceanologist. All she has left him is her ship, a submarine, and a mountain of debt. Natsuki lives with a constant, phantom pain in his missing leg and has given up on his dreams for the future.

Accompanied by his childhood friend Minamo Kamishiro and a mysterious debt collector named Catherine, Natsuki dives to the sunken ruins of his grandmother’s laboratory in search of a rumored treasure to settle his debts. What he finds is not riches, but a mysterious girl named Atri, sleeping peacefully inside a coffin-like machine on the ocean floor.

Atri is an advanced android, so exquisitely made that her appearance and rich emotional expressions are indistinguishable from a human’s. Her memory has suffered from her long slumber, but she recognizes Natsuki as her new master. She tells him that her built-in operational life has only 45 days remaining, but before it ends, she wishes to fulfill the final order left to her by her previous owner. In return for being salvaged, she declares, Until I do, I'll be your leg, becoming his companion and support.

The story unfolds over that one unforgettable summer in the small, slowly sinking seaside town. Atri’s boundless curiosity, quirky personality, and catchphrase "I'm high-performance!" begin to melt Natsuki’s cynical heart. She encourages him to confront his past and re-engage with the world. Together, they reactivate the local school, which is partially submerged and had lost its power, and build a small vortex generator to provide it with electricity. There, they reunite with the gruff but kind-hearted Ryuji Nojima and the studious girl Ririka Nanami. Through these shared moments, Natsuki and Atri grow closer, and he begins to see a future worth fighting for.

As their days pass, the narrative explores several key arcs. The first is the bond of trust and friendship, as Atri helps Natsuki heal from his emotional and physical trauma. This is followed by a golden period of rebuilding and innocent love, where the group works to restore their school and community, and Natsuki falls in love with Atri. However, the idyllic summer is shattered when Natsuki secretly reads Atri’s operational logbook, which clinically records her activities and interactions. Believing the cold text proves her emotions are mere calculations, he feels deeply betrayed and cruelly orders her to stop pretending to have feelings.

This crisis reveals the central conflict regarding Atri’s nature. She is not a standard robot but a technological singularity, a being with genuine self-awareness and emotions. Her past is tragic; she was made for Natsuki's mother, Shiori, and once violently attacked Shiori’s bullies to protect her, leading to her entire model line being recalled. This event also created an enemy in Yasuda, a scientist who blamed Atri for ruining his mentor’s life and seeks to destroy her. The summer culminates in a confrontation with Yasuda at the school, forcing Atri to protect her friends and Natsuki to accept her for who she truly is.

In the final arc, Natsuki learns that his grandmother's true legacy is a plan for a massive floating city called "Iden," a potential solution to the world's flooding. Knowing her time is almost up, Atri chooses to sacrifice herself to become the central control system for Iden, activating it to send power back to the shore and fulfilling her final order. In their last days together, Natsuki and Atri finally confess their true feelings. After she enters her long sleep, a heartbroken Natsuki vows to save the world and one day return to her. Years later, having dedicated his life to robotics and rebuilt human civilization on floating cities, the elderly Natsuki uses his final moments to reunite with a still-sleeping Atri in a computer-simulated reality, where they can finally spend eternity together.