Fuuta Okeya, a 14-year-old student, can see ghosts and wears a bandage on his left cheek to hide his striking birthmark. One day, a girl with a scar on her forehead named Kouko Ishigami, accompanied by a ghost of a tall and friendly man, transfers into his class.

Fuuta quickly takes a liking to Kouko, wondering if it might be love at first sight. After waking up crying from a strange dream involving her, he feels a nostalgic connection to Kouko and becomes determined to befriend her. However, a chain of events forces Fuuta to reveal his birthmark to Kouko, to which she declares him to be the enemy of her life. A furious Kouko explains that the two are bound by reincarnation, and that Fuuta's birthmark is a curse she engraved on him in one of their past lives to recognize and eventually defeat him.

Kouko brings out a circular object made of flames known as the "spirit circle" and attacks Fuuta, pushing him off a flight of stairs. As he falls, Fuuta is thrown back into the insight of one of his previous lives. Spirit Circle chronicles Fuuta's journey back and forth his several past lives as he gradually unravels the mysteries behind his apparent bad blood with Kouko.