In the near future, where much of the Earth's surface has sunk into the sea due to unexplained sea level rise, a young boy named Natsumi Ikaruga, who lost one of his legs in an accident during his childhood, decides to leave the urban life behind and move to a coastal countryside town. Left with nothing but his grandmother's ship and submarine, both belonging to his grandmother who was a marine geologist, and a pile of debt, Natsumi sets out to reclaim the "lost future" by diving towards an underwater warehouse rumored to hold his grandmother's inheritance.
There, he discovers a mysterious girl sleeping in a coffin-like apparatus - Atori. She is a remarkably lifelike and emotionally expressive robot, nearly indistinguishable from a human. Salvaged from the depths of the sea, Atori says, "I want to fulfill the final command Master left behind. Until then, I will be Natsumi-san's legs!"