In the near future, much of the world has been forgotten at the bottom of the ocean due to rising sea levels. Natsuki Ikaruga, who lives in a small town surrounded and stranded by the sea, is invited by a mysterious woman, Catherine, to search for a treasure in his grandmother's house who was a marine geologist. One day, he dives to the bottom of the ocean in a submarine and encounters a mysterious capsule with a girl sleeping inside. The girl was a humanoid so sophisticated that she could be mistaken for a human.

Natsuki happens to see Atri's log that was left open. What was written there was an emotionless record of how she carried out her actions to fulfill Natsuki's desires. Natsuki instinctively rejects Atri and is no longer able to trust anything. Meanwhile, a single letter arrives, and inside there is a report describing the truth behind the Humanoid called Atri.

Atri's last order that was given to her by the capsule was to go to Eden. However, Natsuki and the rest are perplexed by the incomplete set of instructions and don’t know where to even start looking.