The second season is set in even more turbulent times than the first; during the reign of Emperor Gojong, a period where every aspect of Joseon, from financial, military, and economic to the culture was spurred towards modernization. The chaos and confusion resulting from these rapid changes form the background for the crimes that occur, forcing the Byul Soon Geom to be reformed in order to investigate them. The team is led by Jin Moo Young and Han Da Kyung, two people with deep scars and burdens from their past.

The story revolves around criminal investigation and forensic procedures in the late Chosun era, following the activities of an undercover special task force that was established to counter the increasing number of crimes resulting from political turmoil in the period. Kang Seung Jo and Kim Kang Woo lead the team of elite investigators as they uncover the circumstances behind mysterious deaths and other crimes.