With her ability to read minds, Anya Forger is the only one who knows the true identities of her unconventional family. Her pretend father Loid operates as an elite spy code-named Twilight; her mother Yor kills on demand as the assassin Thorn Princess; and their dog, Bond, possesses the gift of precognition. Although they hide the truth from each other, this pretense of a perfectly ordinary family provides Anya with the genuine love and warmth that she longed for as an orphan. Operation Strix—Loid's special mission to avoid potential war by gathering vital information and getting close to the powerful political figure, Donovan Desmond—is only possible if Anya plays her part right. She can either excel academically and become an Imperial Scholar at her prestigious school or make friends with Donovan's son, Damian. Neither is exactly easy, but with her adventurous attitude, Anya throws herself wholeheartedly into her mission as a Forger—all for the sake of international peace.

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.

In the small rural town of Mifuse, time has crawled to a standstill. After an explosion at the city's steel mill, the townspeople realize they are trapped in a mysterious stasis—cutting them off from the rest of the world. With a local elite quick to declare the situation a punishment from God, the community adopts a variety of superstitions to preserve the delicate balance of their circumstances until normalcy is restored. For middle school student Masamune Kikuiri and the other young people of Mifuse, returning to the real world has become nothing more than an illusion. Their senses have gone numb, and it has been years since they have shown any signs of aging. Masamune feels like he has become accustomed to his insecurities and empty existence. However, one day, his classmate Mutsumi Sagami guides him to the fifth furnace of the steel mill, where she shows him a feral young girl who resembles a wolf. This encounter proves to be the impetus in casting a light of change that dispels the shadows that have become Mifuse's reality.