In the near future, a sudden and unexplained sea rise has left
much of human civilization underwater.
Ikaruga Natsuki, a boy who lost one of his legs in an accident when he was young,
returns disillusioned from a harsh life in the big city
to find his old countryside home half-swallowed by the sea.

Left without a family,
all he has to his name is the ship and submarine left to him
by his oceanologist grandmother, and her debts.
In order to restore his dreams for the future that he has lost,
he sets sail to find a treasure rumor says
his grandmother left in the sunken ruins of her laboratory.

But what they find is
a strange girl lying asleep in a coffin at the bottom of the sea, Atri.
She is a robot, with an appearance and wealth of emotions
that would fool anyone into think she's a living, breathing human being.