The disappearance of the Spearhead Squadron beyond the horizon does little to hide the intensity of the Republic of San Magnolia's endless propaganda. Vladilena Milizé continues to operate as Handler One, the commander of yet another dehumanized 86th faction's squadron in the continuous war against the Legion. On the Western Front, Shinei Nouzen and his squad are quarantined in a military base controlled by the Federal Republic of Giad, formerly known as the Giadian Empire. The newly-established government grants the saved Eighty-Six full citizenship and freedom. Housed by the president Ernst Zimmerman himself, the group meets his adoptive daughter and the last Empress, Augusta Frederica Adel-Adler. However, within the calm of this tender society, Shinei and his team feel that their purpose is on the battlefield. Before long, they are once again in the midst of the Legion's onslaught as a part of the Federacy's Nordlicht Squadron, accompanied by Augusta Frederica. But, as history repeats itself, they realize that no matter the side, death and pain on the front lines are the only comfort they know.

When mundane office worker Kiyoshi Adachi turns 30 years old, he discovers that he has gained the ability to read minds due simply to remaining a virgin for his entire life. The caveat, however, is that he must make physical contact with a person to know what they are thinking about. Adachi believes there is no real use for this power until he accidentally hears the thoughts of his coworker, Yuuichi Kurosawa. Charismatic and dependable, Kurosawa is the star of Adachi's team at work, earning praise and admiration from everyone at the office. But deep within, Kurosawa harbors an intense one-sided crush for the gloomy Adachi—a fact that Adachi only learns because of his ability, and knowledge he tries to respectfully disregard. As Kurosawa treats Adachi with kindness and affection he has never experienced before, Adachi finds it increasingly difficult to ignore his coworker's genuine advances.

In 2035, an incident known as “The Burst” occurs at a Japanese research facility, giving birth to the rapidly expanding, consuming, and self-replicating Matter. Snaking its way through the remains of dams and military facilities in the Kurobe Gorge, the hostile Matter is besieged by task forces trying to prevent it from reaching the ocean and mercenaries seeking the truth behind its existence. Aiko Tachibana lives under constant medical surveillance after being rescued from the Matter. She spends her days waiting out her recovery by making paper planes. Soon, her daily life at school is disturbed by the arrival of transfer student Yuuya Kanzaki, who proceeds to point out a number of inconsistencies regarding her body. Why is she never injured, and why does she suddenly no longer need her wheelchair? He claims that there is more to her existence than she has been led to believe, and that she alone holds the key to ending The Burst. With many factions now interested in Aiko, she and Yuuya must gather allies and embark on a dangerous pilgrimage into the heart of the infested gorge before the net can close around them. To escape the conspiracy moving against them, the pair must face off against the Matter—an enemy that flows like water.