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?

Edward Elric, a young, brilliant alchemist, has lost much in his twelve-year life: when he and his brother Alphonse try to resurrect their dead mother through the forbidden act of human transmutation, Edward loses his brother as well as two of his limbs. With his supreme alchemy skills, Edward binds Alphonse's soul to a large suit of armor. A year later, Edward, now promoted to the fullmetal alchemist of the state, embarks on a journey with his younger brother to obtain the Philosopher's Stone. The fabled mythical object is rumored to be capable of amplifying an alchemist's abilities by leaps and bounds, thus allowing them to override the fundamental law of alchemy: to gain something, an alchemist must sacrifice something of equal value. Edward hopes to draw into the military's resources to find the fabled stone and restore his and Alphonse's bodies to normal. However, the Elric brothers soon discover that there is more to the legendary stone than meets the eye, as they are led to the epicenter of a far darker battle than they could have ever imagined.

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.

Hakuo Academy was once a respected school where many students dreamed of being admitted. Now, its rival academy Seishikan is on a mission to assimilate all other schools, and Hakuo Academy is its next target. Supported by the fearsome Yasha clan, Seishikan students frequently visit Hakuo's campus to assault and forcibly convince their best students and athletes to transfer to Seishikan. Desperate to preserve their legacy, Hakuo Academy enlists the help of Kojirou Fuuma—the only member of the once-legendary Fuuma clan still living in their ancestral village. Kojirou will stop at nothing to defend Hakuo against the Yasha clan, whom the family has feuded with for generations. But will that be enough to stop Seishikan's aggression?