"ATRI: My Dear Moments" is a science fiction visual novel adaptation set in a near-future world where rising sea levels have submerged much of the Earth's landmass. The story centers on Natsuki Ikaruga, a young boy who returns to his coastal hometown after a personal tragedy. His mother, a renowned marine engineer, has passed away, leaving him with a dilapidated house and a mountain of debt. To repay the debt, Natsuki decides to salvage valuable materials from the sunken ruins of the town with the help of a robotic companion.

The narrative takes a significant turn when Natsuki encounters Atri, a highly advanced humanoid robot with a strikingly human appearance. Atri was created by Natsuki's mother and possesses a unique ability to experience emotions, a rarity among robots. Despite her mechanical nature, Atri exhibits a cheerful and curious personality, often displaying childlike wonder and a strong desire to understand human emotions. Natsuki reluctantly agrees to work with Atri, and the two form an unlikely partnership as they navigate the challenges of their underwater salvage missions.

As the story progresses, the relationship between Natsuki and Atri deepens, exploring themes of humanity, loss, and the meaning of existence. Atri's presence forces Natsuki to confront his own emotional struggles and the lingering pain of his mother's death. Meanwhile, Atri grapples with her own identity, questioning what it means to be "alive" and whether her emotions are genuine or merely programmed responses. The narrative is punctuated by moments of introspection and emotional weight, as both characters come to terms with their pasts and their evolving bond.

The supporting cast includes Minamo Kamishiro, a childhood friend of Natsuki who harbors unspoken feelings for him, and Ryuuji Takizawa, a local mechanic who provides technical assistance and comic relief. These characters add depth to the story, offering different perspectives on the central themes and contributing to the world-building of the submerged town.

The plot is driven by a mix of personal drama and external challenges, including the harsh realities of a world grappling with environmental collapse. The underwater salvage missions serve as a backdrop for the characters' emotional journeys, blending action and introspection. The story culminates in a poignant exploration of love, sacrifice, and the enduring impact of human connections, leaving a lasting impression on the audience.