In 1983, twenty-one South Korean special forces soldiers are sent on a covert mission only to be deliberately abandoned and killed by their own government officials. The sole survivor, Lee Jin Pyo, survives but is left for dead by a corrupt group of five powerful politicians and military leaders who orchestrated the betrayal. Consumed by a need for retribution, Jin Pyo kidnaps the infant son of his deceased best friend, Park Moo Yul, and raises the boy in a secret, brutal compound in the jungles of Southeast Asia. He names the boy Lee Yoon Sung and trains him for nearly three decades to become the ultimate instrument of vengeance.

Twenty-eight years later, Lee Yoon Sung (Lee Min Ho) returns to Seoul armed with a doctorate from MIT, flawless combat skills, and a meticulously crafted identity as a naive but gifted data analyst for the Blue House, the presidential residence. By day, Yoon Sung poses as a calm and gentle IT expert, working alongside his childhood acquaintance, the spirited and athletic presidential bodyguard Kim Nana (Park Min Young). By night, he becomes the City Hunter, a mysterious vigilante who uses his elite training and access to government secrets to systematically dismantle the five men who murdered his father.

Unlike the private detective of the original Japanese manga, this City Hunter is a ghost seeking political retribution. Each of the five targets holds a high position in society, ranging from a corrupt defense minister to a ruthless factory owner, and each is guilty of crimes ranging from embezzlement to murder. Yoon Sung engineers elaborate schemes to expose their corruption to the public, forcing them to face justice in ways their power and status had previously prevented. However, he soon discovers that his surrogate father, Jin Pyo (Kim Sang Joong), who commands him from the shadows, is not interested in legal justice. Jin Pyo’s thirst for blood threatens to consume everyone, including the innocent people Yoon Sung has come to care about.

As Yoon Sung closes in on the final target, the sitting President of South Korea, he uncovers a devastating secret: the President is his biological father, making Jin Pyo’s ultimate plan a cruel act of forcing a son to kill his own parent. This revelation forces Yoon Sung to break from his training and choose his own path. Meanwhile, his relationship with Kim Nana deepens from reluctant allies into a romantic partnership, complicated by the secret of his identity and his mission of revenge. After a climactic confrontation that leaves Jin Pyo apparently dead and Yoon Sung critically injured, the series concludes with the President stepping down to face prosecution, and the City Hunter disappearing, with Yoon Sung and Nana finally able to pursue a life free from the conspiracy of the past.