Yozora Fujimitsu enrolls at North Gate National Military Academy, a prestigious institution for the children of the countrys elite, hiding his true identity in order to search for his missing younger brother, Izumi. Although Yozora possesses the beauty and intelligence that the academy values above all else, he immediately feels uneasy and out of place, convinced that the school harbors a significant secret. He is assigned to room with Arisu Kagamihara, a timid student labeled an underachiever who is subjected to bullying by his peers.

As Yozora becomes determined to expose the academys hidden truths, he is pulled into a vortex of violence and deceit fueled by the desire to preserve tradition at any cost. The story follows the unlikely pairing of Yozora and Arisu as their meeting begins to change the fate of the school and their country. Initially belonging to the lowest ranked Class 9, the two eventually transfer to Class 0, where the elite students gather, in their pursuit of the true enemy, Kuuga Saionji, who is hidden within the school. There, they face intense challenges from their unique and highly capable classmates. As they close in on Saionji, they encounter repeated interference from an enemy who does not reveal themselves, and the truth that comes to light is described as extremely cruel.