On the first day of junior high school, Mato Kuroi happens to run into Yomi Takanashi, a shy, withdrawn girl whom she immediately takes an interest in. Mato tries her best to make conversation with Yomi, wanting to befriend her. At first, she is avoided, but the ice breaks when Yomi happens to notice a decorative blue bird attached to Mato's phone, which is from the book "Li'l Birds At Play." Discovering they have a common interest, the two form a strong friendship.
In an alternate universe, the young girls exist as parallel beings, Mato as Black★Rock Shooter, and Yomi as Dead Master. Somehow, what happens in one world seems to have an effect on the other, and unaware of this fact, the girls unknowingly become entangled by the threads of fate.
Long ago, all humans lived beneath the sea. However, some people preferred the surface and abandoned living underwater permanently. As a consequence, they were stripped of their god-given protection called "Ena" which allowed them to breathe underwater. Over time, the rift between the denizens of the sea and of the surface widened, although contact between the two peoples still existed.
This show follows the story of Hikari Sakishima and Manaka Mukaido, along with their childhood friends Chisaki Hiradaira and Kaname Isaki, who are forced to leave the sea and attend a school on the surface. There, the group also meets Tsumugu Kihara, a fellow student and fisherman who loves the sea.
Hikari and his friends' lives are bound to change as they have to deal with the deep-seated hatred and discrimination between the people of sea and of the surface, the storms in their personal lives, as well as an impending tempest which may spell doom for all who dwell on the surface.
A young boy called Eita enters high school aiming for the National University School of Medicine. Because of his parents' divorce and his goal, he shuns anything to do with romance or love. One day Masuzu, the school beauty with the silver hair, who's just returned to the country, enters his life in a most unexpected way. Chiwa, his childhood friend since elementary school, will not let this go without a fight.