Fuuta Okeya is a 14-year-old boy who can see ghosts and conceals a noticeable birthmark on his left cheek with a bandage. One day, a new student named Kouko Ishigami, who has a scar on her forehead and is accompanied by the ghost of a tall, friendly man, transfers into his class.
Fuuta quickly develops a fondness for Kouko, thinking it might be love at first sight. After waking up in tears from a strange dream involving her, he feels a sense of nostalgia and becomes determined to become her friend. However, a series of events forces Fuuta to show his birthmark to Kouko, upon which she declares him her lifelong enemy. An enraged Kouko explains that the two are connected through reincarnation, and that Fuuta's birthmark is a curse she placed on him in one of their past lives so she could recognize and ultimately defeat him.
Kouko summons a circular, flame-based object called the "spirit circle" and attacks Fuuta, shoving him down a staircase. As he falls, Fuuta is hurled into the memory of one of his previous lives. Spirit Circle follows Fuuta as he travels back and forth through his various past lives, slowly uncovering the truth behind his apparent feud with Kouko.