In the near future, a sudden rise in sea levels floods the majority of the world and ends human civilization as we know it, forcing humanity to eke a living on what little dry land remains. Natsuki Ikaruga is a young man living under difficult circumstances in this new world. He has lost one of his legs in an accident which can only be replaced with a crude prosthetic, and he suffers constant bouts of phantom pain. One day, though, Natsuki rummages through his recently deceased grandmother's belongings to pay off a debt, only to awaken a young android girl named Atri, who will go on to change his life forever.