Secret Investigation Record is based on cases detailed in the Annals of Joseon History with a bizarre twist; these incidents incorporate mysterious, supernatural elements that cannot be explained through science. Kim Hyung Do is an inspector of the state whose single-minded focus on his investigations into administrative misdeeds bring him into direct contact with these strange mysteries. Heo Yoon Yi is a government employee who aids him and attempts to understand these scientific impossibilities with an open mind, in contrast to his cynicism.

Eun Seo and Eun Young both grow up at the church orphanage. Eun Seo falls in love with Kim Min Woo and had his son. But unfortunately Min Woo and their son die in a car accident on their way to meet Min Woo's parents. This accident causes Eun Seo forget about her past life and her memory. Min Woo's brother, Min Ho, returns to Korea and becomes the heir to the family congomorate after Min Woo's death. Eun Young assumes Eun Seo's life and pretends to be her. Min Ho later meets and falls in love with Eun Seo.