Rune Balot is a down-and-out teen prostitute in Mardock City. One day, she's picked up by an ambitious casino manager named Shell who gives her everything she could want. Renewed by a false innocence, a false past, and now the false life Shell has given her, Balot feels grateful. However, she can't help but be curious about why he's done so much for her, so she does some research about his past on a computer. This turns out to be a mistake which will change her life greatly. When Shell finds out what she's done, he attempts to burn her to death by blowing up her car.

Due to the high crime rate in Mardock, a new law called "Scramble 09" has given police carte blanche to take extreme and otherwise illegal measures to revive crime witnesses. With this in mind, they allow a professor to bring Balot back from the brink of death by reassembling her entire body with reinforced synthetic fiber. When she finally wakes up, her confused mental state eventually turns toward revenge as Shell is revealed as her killer.

(Source: Nippon Cinema)

Kokone Morikawa has a strange napping disease that distracts her from reality, one that makes the world of her dreams and the real world near indistinguishable. In reality, she is an average high school student preparing for her university entrance exams; but in her dreams she is a magical princess of Heartland, a machine-driven future where the use of artificial intelligence is forbidden. Within the seemingly imaginary dreamland, Kokone discovers more about her family's past and the secret that her father, a talented mechanic, has tried to protect her from. However, as the events between two worlds intertwine, she must now protect the secret from villainous entities, both dream-like and terrifyingly real.

Tucked away in the darkest depths of this world, tales of the bizarre and the supernatural quietly unfold. These inexplicable stories are chronicled throughout the pages of a certain strange encyclopedia, sheltered within a crumbling, decrepit building. Do you dare to open its cover and experience the horrors firsthand? Each of the macabre tales held within the book's pages details some unusual, surreal experiences that often come to a gruesome end. A man searches for his adulterous wife, only to find himself at the mercy of otherworldly visitors; a boy befriends a snowman who harbors a sinister secret; crop circles suddenly form on a family farm, created by some unexpected visitors; hidden in plain sight, menacing mechanical beings continue on undetected. In all of these horrifying stories, nothing is as simple as it seems, revealing a terrifying darkness that perhaps might have been best left alone. [Written by MAL Rewrite]

Following the first season, Tomoharu is now faced with a dilemma: if he doesn't form a contract with an "akuma," he risks losing his dear friend Takatsuki. However, doing so would compromise his own existence as it would result in him and his ghost friend Misao becoming an Asura Cryin'—mankind's biggest threat, according to their school's presidents. To make the decision even harder, Tomoharu and Misao have recovered some of their past memories—memories of a world that they didn't even know existed.