تلتحق تايغا، الابنة الكبرى لرئيس عائلة سينغوكو، للصفّ أ في أكاديميّة ميهاما. يقوم هاروتو بتعيين كريس كضابطة أعلى مسؤولة عن تايغا ورعايتها. لا تحبّذ تايغا أن تُعاملها كريس كطفلة. تتدرّب تايغا لتصبح مُؤهّلة وتنسجم مع بقيّة طلّاب الصفّ.

A terrorist attack transpires at the medical university Taiga visited. The perpetrators are members of a new religious group seeking to obtain a virus to be used for bioterrorism. The United Nations decides to conduct an air strike to prevent the virus from spreading worldwide. Receiving the news, Class A was ordered to stay put. However, Chris ignores the order to rescue Taiga on her own.

Chris fights the terrorists with explosives but gets shot. Class A heads to the scene after receiving a warning. Class A's operation begins.

Murasaki's sister, Yuuki, returns to Class A. Rena is annoyed with her, and Murasaki doesn't seem herself. What happened to the sisters in their past?

Several years before, Haruto visited Yuuki's village to learn "Phantom Blade." One day, the village got ambushed, and Murasaki suspected Haruto.

Haruto was born by an experiment. He was raised by Ichiru, Nogami, and Aoi Aoi, a group of assassins. Let us look into how "Haruto Aoi" came about.

Phantom Trigger got a mission to destroy a religious group. Who awaited the team was a very familiar face.

Arisaka must decide on Class A's overseas deployment request. Enishi and Chloe awaits Class A.

All SORD forces are called upon. Haruto encounters Chloe. He points his sword to his archenemy who killed Aoi.

Patrick and Bruno meet a group of young Sisters in a dugout. We just want to live...

As members of Mihama Academy fight their own battles, former Phantom Trigger makes a big decision.

All SORD forces except Class A retreat. Rena is remembering the time when she was picked up by Haruto.

The battle is coming to an end. This is the story of Phantom Trigger drenched in blood and smoke.