After overcoming various tumultuous events, mercenary sergeant Sousuke Sagara of Mithril and Whispered school girl Kaname Chidori return to their normal high school lives. Sousuke continues his efforts to assimilate with the civilian population and manage his mission at the same time, while Kaname attempts to support his endeavors (even though his antics often drive her up a wall). However, as their lives calm, new problems begin to appear. The appearance of an independent terrorist organization known as Amalgam and internal conflicts within Mithril threaten to wreak unity into a series of failures and betrayals. And new, powerful Arm Slave models only worsen the situation when the world's peace is at stake. As Kaname and Sousuke face their own inner battles amidst life-threatening fights, will they be able to make the right choices and change their future?

Mithril, a covert military institution using state-of-the-art technology to combat terrorist operations, assigns a specialized team to a sensitive mission. Under the command of superior officer Melissa Mao, sergeants Sousuke Sagara and Kurz Weber must secretly protect Kaname Chidori—a teenage girl who unconsciously holds breakthrough scientific knowledge and is considered a Whispered—from intelligence agencies and other organizations pursuing her abilities. While Kurz and Melissa are to assist him remotely, Sousuke enrolls at Kaname's high school as one of her classmates to closely monitor her. However, his militaristic upbringing and poor social skills lead to a difficult adjustment to civilian life. Not only does he attract unnecessary attention, but his actions frequently make Kaname suspicious of him. Despite the earnest attempts to fulfill his duty, a terrorist ambush further complicates Sousuke's task. Recognizing the vicious mastermind behind the assault, Sousuke abandons his orders to ensure Kaname's safety.

Third-year high school student Jirou Yakuin is in love with his childhood friend and classmate, Shiori Sakurazaka. Thus, he hopes to be paired with her for the marriage practical: their school's practice of randomly selecting boy-girl pairs to live as pretend married couples while monitoring and rating them on how close they have gotten. Meanwhile, the lively Akari Watanabe wants to be assigned to her crush, the popular and good-looking Minami Tenjin. Much to their dismay, Jirou and Akari find out that not only have they been paired together, but so have Shiori and Minami! Determined to be with their crushes, Jirou and Akari strive to earn as many points as possible, as the top 10 pairs earn the right to switch their partners—so long as both couples agree.

In Japan, there exists a government agency known as the Supernatural Disaster Countermeasures Division (SDCD), whose duty is to protect the citizens from creatures unseen. They are able to dispatch these monsters swiftly and without alerting the general public. But currently, they face a different challenge: the betrayal of one of their own. After the death of her mother several years ago, Kagura Tsuchimiya has been fostered by the Isayama family and forms a close sister-like bond with their daughter Yomi. The two become inseparable, and together they work for the SDCD as highly skilled exorcists. However, as the stress and consequences of their sacred duty weigh on them both, and family politics come into play, Kagura and Yomi begin to slowly drift apart. One of them grows earnestly into her role as an exorcist, and the other heads down a dark path from which there may be no redemption.