Fuminori Sakisaka is a young medical student, whose life is changed when he gets in a traffic accident which kills his parents and leaves him heavily injured. Fuminori undergoes experimental brain surgery to save his life, but the surgery has an unintended side-effect - it creates a form ofagnosia, causing his senses to become "warped". He perceives the world as a hellish nightmare with a black sky and buildings covered in pulsating flesh, where all the streets and building interiors are splattered with blood, giant organs and cartilage. Ordinary people appear to him as grotesque, giant grub-like monsters with a hideous stench, and even food that he used to like now tastes utterly disgusting.
As he contemplates suicide in the hospital, Fuminori meets a beautiful, human looking girl among the flesh-covered walls. She introduces herself as Saya, and is apparently looking for her father. Fuminori does not want to be separated from Saya, and asks her to live with him. She agrees.
However, just as Fuminori sees normal things as monstrously twisted abominations, ordinary observers are able to see that Saya is actually a hideous creature from another universe. She is rarely ever seen by anyone but Fuminori, and those that do see her are immediately killed and consumed by her, usually after being driven insane by her hideous appearance. Though her true form is never directly shown, it is described in text, and she is similar in appearance to the misshapen blob-like monstrosities which haunt Fuminori's world. The ultimate goal of her life is to spread her life-form into this universe by transforming the native life-form with the highest level of intelligence: the human being. She learned everything about humanity from her "father", an eccentric Bio-medical scientist named Masahiko Ōgai, the first person to interact with Saya. She finds out the motive of human reproduction is "love", and the process is carried out by females. Consequently, she considers herself as a girl, looking for "love" to prepare for the final reproduction. However, because of her grotesque appearance, she had no chance to succeed - until she met Fuminori.
After her first contact died, she stayed in the hospital to continue her study and to look for the next relationship with a human being, which unfortunately results in a horror story in that hospital. Fuminori's experience also provides her the chance to learn the skills of modifying brains and bodies of human beings.
The truth is revealed when Fuminori comes home to see Saya eating the slime-covered corpse of Ōmi, a girl he knows which appears as a yellow-green jelly-like thing in Fuminori's eyes. The smell and texture was described by Fuminori as "herb-like scent, looks like a variety of succulent fruits". When he tries it, he actually finds the human flesh delicious due to his twisted senses.