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 sets his heart on creating a tidal power generator that utilizes the ebb and flow of the ocean's tides. He dives back into the ocean to find some materials and salvages some resin from the ruins of Ryuuji's family's factory. As soon as he gets back he gets to work. As they are working, Natsuki and Ryuuji exchange heated opinions over how the generator should be built. Atri intervenes and the two guys become closer friends. Meanwhile, a suspicious-looking character peeks at them from outside of the school...

If Natsuki sells Atri, he can get batteries. However, he can no longer think of Atri as just an average humanoid. While he's deep in thought on the dock, looking out at the ocean, Natsuki finds Catherine floating in the water. She is completely intoxicated, and Natsuki and Atri take her in. But right at that time, the sound of a gunshot echoes within the silent ship.