Yashima is a city of 2 halves. Upper Yashima is where the humans safely live in their homes without much threat or worry. Lower Yashima on the other hand, is where humans who aren't so lucky live alongside the half beast-like beings known as kemono, and creatures known as makatsuhi. Creatures without any emotions or signs of intelligence that seem to function purely on instinct, and prey on humans and kemono alike. The only thing protecting humans from makatsuhi are the kemono of Zero Squad. A special class within Akatsuki Academy that gathers up kemono with special powers and trains them on how to use their powers to protect the humans and kemono alike from the threat of the makatsuhi. The problem is that humans see kemono as dangerous beasts just like the makatsuhi. Yuu is a human who has always had impossibly bad luck wherever he goes. On his way to a new school, he gets kidnapped by kemono who hold a grudge against humans, gets attacked by a makatsuhi, and is helped by a kemono named Riko. The next thing he realizes, Yuu has been transferred into Zero Squad and is forced to learn to fight.

This is the story of Zero Squad and their battle to find their place in a world that sees them as a threat.