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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 Kuroh Yatogami. But Shiro learns that Kuroh is after his life as well, and so he uses his wits to flee the scene.

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

Kuro 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 Kuro, 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.