Having reached professional status in middle school, Rei Kiriyama is one of the few elite in the world of shogi. Due to this, he faces an enormous amount of pressure, both from the shogi community and his adoptive family. Seeking independence from his tense home life, he moves into an apartment in Tokyo. As a 17-year-old living on his own, Rei tends to take poor care of himself, and his reclusive personality ostracizes him from his peers in school and at the shogi hall. However, not long after his arrival in Tokyo, Rei meets Akari, Hinata, and Momo Kawamoto, a trio of sisters living with their grandfather who owns a traditional wagashi shop. Akari, the oldest of the three girls, is determined to combat Rei's loneliness and poorly sustained lifestyle with motherly hospitality. The Kawamoto sisters, coping with past tragedies, also share with Rei a unique familial bond that he has lacked for most of his life. As he struggles to maintain himself physically and mentally through his shogi career, Rei must learn how to interact with others and understand his own complex emotions.

According to the Republic of San Magnolia, their ongoing war against the Giadian Empire has no casualties—however, that is mere propaganda. While the silver-haired Alba of the Republic's eighty-five sectors live safely behind protective walls, those of different appearances are interned in a secret eighty-sixth faction. Known within the military as the Eighty-Six, they are forced to fight against the Empire's autonomous Legion under the command of the Republican Handlers. Vladilena Milizé is assigned to the Spearhead squadron to replace their previous Handler. Shunned by her peers for being a fellow Eighty-Six supporter, she continues to fight against their inhumane discrimination. Shinei Nouzen is the captain of the Spearhead squadron. Infamous for being the sole survivor of every squadron he's been in, he insists on shouldering the names and wishes of his fallen comrades. When the fates of these young souls from two different worlds collide, will it ignite the spark that lights their path to salvation, or will they burn themselves in the flames of despair?

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.