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.

When Natsuki comes to the rescue for the now-beaten-up Atri, he becomes the next target of Yasuda’s acts of violence. With the onslaught of consecutive attacks, he finds himself also beaten up, just like Atri. Before Yasuda can inflict any more pain, Atri, unable to tolerate watching any longer, raises her fist against a human once more.

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.