Asako Kusakabe rescues a young Yuuji from terrorists on a certain mission. She has evaded death as a soldier time and time again, and on a whim decides to become Yuuji's guardian. Although she partially forces it, and despite her coworker JB's concerns, the awkward female soldier and young man begin to live under the same roof.
Asako's poor health begins to interfere with her work. Yuuji senses her change in condition, and as he covers for her, he starts to think he may have found his life's meaning. Asako tries to respect Yuuji's resolve, but JB, who watches over both of them closely, is apprehensive about Yuuji's attempts to return to that violent world.
Yuuji goes to America to follow the same path as Asako, and through his rigorous military life meets and forms a deep bond with war buddies who go through the same joys and sorrows.
Yuuji moves forward on his path as a soldier to protect "an important woman": Asako. However, she leaves his side without waiting until he's reached maturity. Yuuji is yet again tormented by a sense of helplessness, but is saved by Asako's parting words and begins to be able to walk on his own two feet once more.
After Yuuji suddenly disappears, the girls at Mihama Academy notice him on the TV screen. What's more, it's being reported nationwide that he's a suspect in a terrorist plot which will likely turn into an international incident.
After Yumiko gets in touch with the informant "Jimmy," she and the other girls at Mihama Academy learn that the current situation is even worse than they thought. Although they have lost Yuuji and have been driven from the academy, they secure a new base of operations and plan a rescue mission for him.
A formless supporter, "Thanatos," suddenly supports Amane and the others. "Her" objective is also to liberate and rescue Yuuji Kazami. Thanatos and the Mihama girls' interests align and begin preparing to execute their mission. The girls are perplexed by Thanatos's seemingly cryptic instructions that unfold via cell phone, but they bring the girls better results than they ever expected in bringing their goal to fruition.
The international terrorist Heath Oslo uses nuclear weapons as a shield to threaten the nation. The nation plans to make Yuuji a human sacrifice in their dealings with Oslo. There is no other way to save Yuuji from this crisis but to rescue him as he is transferred from Ichigaya to Akasaka.
The Mihama girls have executed their intense getaway and have rescued Yuuji. Waiting at their goal is Kazuki Kazami, who lived as the core of Thanatos for a long time. This unexpected encounter leaves Yuuji and Amane unable to hide their surprise, but circumstances don't allow them time to savor their emotional reunion.
Tartarus, a gigantic, man-made island, floats on the Pacific Ocean. It is both the adversary of society, and the castle of Heath Oslo, Yuuji Kazami's mortal enemy. Oslo quietly awaits the moment Yuuji Kazami, the final key he needs to fulfill his ambitions, appears before him once more.