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Ashinaka High School is known for its unique setting: the entire campus is built on an island. Yashiro Isana, aka Shiro, is having lunch with a cat on one of the school rooftops. After his lunch break, Shiro goes on an errand for his classmate Kukuri to prepare for their upcoming school festival, only to be chased by some intimidating-looking men.

Shiro manages to outrun HOMRA with help from a young man named Kurou Yatogami. But Shiro learns that Kurou is after his life as well, and so he uses his wits to flee the scene. Meanwhile, unknown to Shiro, his cat has suddenly turned into a beautiful girl.

After an all-night chase, an exhausted Shiro, Kurou, and Neko decide to make a temporary truce to have breakfast. As they eat, Kurou gives Shiro more background about the seven Kings and the Clans they lead. Kurou then adds that Shiro is suspected of murdering one of HOMRA’s Clansman, which Shiro strongly denies doing.

Kurou threatens to kill Shiro unless he can prove that he is not the one who killed Tatara Totsuka. Determined to prove his innocence, Shiro begins searching for anyone who can confirm his alibi on the night of the killing. Meanwhile, the Blue and Red Clans follow their own leads to the suspect, which all point to Shiro.

Shiro is relieved after proving his alibi to Kurou, only to find a bloodstained shirt tucked away in his closet. Meanwhile, both SCEPTER 4 and HOMRA have entered Ashinaka High School in search of Shiro.

Shiro begins to question his own identity after realizing there is an inconsistency between what he remembers and what actually happened. Meanwhile, Lieutenant Seri Awashima of SCEPTER 4 makes a visit to the bar owned by Izumo Kusanagi, where she learns more about the history behind HOMRA and the strong bond they share.

Unable to find any traces of his own past, Shiro begins to believe that the person known as Yashiro Isana may not have existed. As Shiro and Kurou try to think of what to do next, SCEPTER 4, led by the Blue King Reishi Munakata, arrives to apprehend them.

Neko undoes the spell placed on Shiro to help him remember who he is. But other than a brief image of being thrown from an airship by a mysterious man, Shiro remains in the dark. Determined to regain his memories, Shiro takes the risk of contacting Reishi, the Blue King, who could lead them to the mystery man.

The Blue King, Reishi, accepts a proposal from Shiro to carry out an air mission to restrain the Silver King, Adolf K. Weismann. However, the mission is abruptly interrupted when the Silver King’s airship self-destructs. The following day, Reishi pays a visit to the Gold King, where he discovers the remains of the Silver King. In the meantime, an unknown force makes contact with the detained Mikoto.

The Red King, Mikoto Suou, is contacted by a man claiming to be the killer of Tatara Totsuka. By utilizing his power, Mikoto escapes his prison cell to hunt down the killer at Ashinaka High School. While HOMRA occupies the school property to conduct their search, the Blue King, Reishi Munakata, makes one final attempt to reason with the Mikoto.

Tension builds overnight as HOMRA occupies the island of Ashinaka High School, prompting SCEPTER 4 to secure the bridge at the island’s entrance. The following morning, a sudden explosion initiates a clash between the two forces. In the meantime, Shiro returns to the Red occupied island and reunites with Kukuri at the battle-ravaged school building.

The war between the Blue and Red clans intensifies as Mikoto and Reishi finally face off. With his memory restored, Shiro introduces himself to Kurou and Neko as Adolf K. Weissmann, the Silver King.