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.

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. Meanwhile, the battle between Mikoto and Reishi continues, with the Red King’s Sword of Damocles slowly reaching its limit. With time running out for all sides, what fate awaits these four kings?

A year has passed since the School Island incident, where four of the seven kings fought for their lives to stop the evil Colorless King. Since then, Silver King Yashiro Isana has gone missing and the Green Clan JUNGLE has become more active in spreading their influence over the community, much to the annoyance of Blue Clan SCEPTER 4 and Red Clan HOMRA.

Hoping to learn more about his recent encounter with JUNGLE, Blue King Reisi Munakata summons Kuro to SCEPTER 4; Neko waits at HOMRA's home base for her partner.

In a flashback, Mikoto surrenders to Reisi rather than fight him. As Reisi interrogates Mikoto, he wonders why the Red King has yet to choose his successor. Meanwhile Shiro asks Kuroh who were the people with powers chasing him and the "Kings". Kuroh reveals Japan is secretly being ruled by seven psychic clans called the Seven clans of Color, each ruled by a King. Unlike the Red Clan Homura and Blue Clan Scepter 4, whose clans posses the power of fire and ice respectively, his late master's clan, the Colorless Clan, have the power of premonition. Before his master, Ichigen Miwa passed away, he had a vision that his successor, Shiro, might become evil, which Kuroh is tasked to kill him if there is proof. Shiro convinces Kuroh the video released by Homura might be a fake and he shouldn't use that to quickly judge him that he is evil without knowing him first. Kuroh agrees to stop attacking him and get know to Shiro but if he ever turns evil, he will kill him.

Shiro desperately tries to find a possible alibi in order to prove to Kuroh he was not there during the time of the video. Meanwhile, Homura and Scepter 4 are able to close in on Shiro's whereabouts. Thanks to Kukuri who is able to provide proof that Shiro was with her during the time of the shooting, Shiro and his friends prepare for the school festival. When he goes to his dorm and opens his closet, he is shocked to discover a bloody school uniform that matches the murderer's picture which leads Shiro to rethink the whole situation. As he contemplates, Yata and Kamamoto arrives at Ashinaka.

Shiro, Neko and Kuroh heads to the city to buy more fireworks for the festival. Meanwhile Seri and Saruhiko arrives at Ashinaka and orders the principal to give them all their information on Shiro, unaware he had just left. While Saruhiko illegally access the student council's computer to find Shiro in the student database, Misaki and Rikio asks the students for information about Shiro but due to their looks and Misaki's temper, they only scared them. Saruhiko soon encounters Misaki and Rikio, where he mocks and insults his former friends which angers Misaki to fight him. The fight is soon stopped by Seri who orders Saruhiko to returned to Scepter 4 as neither the school or it's database has a record of Shiro being a student at Ashinaka. When Misaki asks a female student about Shiro before leaving, the student, Kukuri tells him she has no idea who Shiro is.

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.

Scepter 4 has finally tracked down Shiro as they prepare to arrest him. Neko creates an illusion in order for Shiro to escape, but is easily thwarted by Reisi who reveals that she has the power to manipulate people's minds by giving them false memories. While Kuro fights Reisi, Neko escapes with Shiro. When Kuro is nearly defeated, Shiro appears and reveals his true identity to them as the new Colorless King, using his power to let him, Kuro, and Neko escape. After they get away, Shiro convinces Neko to undo the amnesia spell on him to find out the truth.

Shiro finds out from his recovered memory about being involved with the Silver King. He contacts Reisi about his findings, while the rest of Scepter 4 tracks his location. When they reach the location they find out that the phone call was rigged by Shiro. Meanwhile, Reisi send his forces towards the Silver King's airship to take him into custody, unaware that Shiro, Kuroh, and Neko are secretly on a plane also heading to the ship, but as they approach, the Silver King sets off an explosion.

In the year 1945 at Dresden, Germany, Adolf and his older sister experiment a relic called the Slate that gives people magical powers. During a bombing raid, Adolf's sister is killed but he himself survives thanks to the power of the Slate. Distraught over her death, Adolf leaves Germany and brings the Slate into his airship Himmelreich. Back in the present, Reisi visits the Golden King, Daikaku Kokujōji, wanting to confirm if the immortal Adolf is really dead. Believing Adolf is faking his death, Reisi orders Scepter 4 to keep on eye on him. Meanwhile, a mysterious man calls Mikoto from Ashinaka where he mocks him and claims he killed Tatara. Angered, Mikoto breaks out of prison and overpowers Scepter 4. Reuniting with the rest of Homra, Mikoto and gang heads to Ashinaka.

Homra takes over Ashinaka campus as they search for Shiro, Totsuka's killer. Scepter 4 also arrives and are ordered to stand by before they attack. Reisi confronts Mikoto, telling him his actions have gone too far. Reisi is willing to forgive Homra if they leave the campus and Scepter 4 will hunt down and punish Shiro for them but Mikoto refuses. Reisi warns Mikto if he kills Shiro, a King, he will lose control of his powers. Meanwhile, Shiro, Kuroh, and Neko manages to sneak into campus and decides to rescue their friends.

After a confrontation between the Blue and Red Kings, Homra and Scepter 4 forces begin to clash. Mikoto goes off on his own to hunt down Shiro where he eventually finds him with Neko, Kukuri, and Kuroh. During the struggle between Mikoto and Kuroh, Reisi intervenes and strikes at Mikoto. Shiro, Kuroh, Neko, and Kukuri make the chance to escape when all of a sudden, Kukuri stabs Shiro. It is revealed that she is possessed by a White Fox spirit out to target Shiro. The possessed Kukuri escapes while Shiro begins to remember his memories and awakens as Adolf K. Weismann, the Silver King.

Shiro, with his recovered memories as the Silver King reveals that his current body was once possessed by the new Colorless King (White Spirit Fox) who wanted to take over his original body to gain his power, but to no avail instead just possessing his body and not his powers. At that moment, his spirit had jumped to the Colorless King's recent body where he got amnesia. He uses his power to let the students of Ashinaka escape, at the same time cooperating with Kusanagi and Awashima to stop the two clansmen from fighting. Shiro asks Neko to become his first clansmen, and uses her power to find the Colorless King. After she successfully locates him, she passes out and Shiro leaves to confront the Colorless King.

Reisi and Mikoto continue their fight while Shiro tries to catch the Colorless King who's still in Kukuri's body. Helped by Kuro, who becomes his clansman, Shiro tricks the Colorless King to get out from Kukuri's body and trap him into his own body. Shiro teleports to where Mikoto and Reisi are and tells Mikoto to kill him while the Colorless King is still trapped in his body as only a king can slay another king. Mikoto does so, finally avenging Tatara's death but his Weismann level reaches its limit, which his Sword of Damocles is about to crash into the campus. Reisi is forced to kill Mikoto to prevent that which the latter shares some words with his fellow king before passing away peacefully. The Homra gang honors their late leader with a battle cry as they lose their powers. Neko and Kuroh escape the island, still believing Shiro is still alive.