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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. Shiro goes on an errand for his classmate Kukuri.

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.

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.

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.

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.

Unable to find any traces of his own past, Shiro begins to believe that the person known as Yashiro Isana may not have existed.

The Blue King, Munakata, 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 Red King, Mikoto Suoh, 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.

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.

The war between the Blue and Red clans intensifies as Suoh and Munakata finally face off. Meanwhile, an unexpected attack triggers Shiro to regain his lost memories.

Shiro regains his memory and power as the Silver King. After evacuating everyone on the island to safety, Shiro sets out to settle his score with the real Colorless King.