In 1983, the South Korean president and his delegates are visiting Burma when a bomb planted by North Korean agents explodes, killing some high-ranking officials. This historical event is called the Rangoon bombing (also known as the Rangoon incident). To strike back, five South Korean officials plan a covert operation, codenamed "Operation Cleansweep", to enter North Korea and kill several top members of the North's high command. Lee Jin-pyo (Kim Sang-joong) and Park Moo-yeol (Park Sang-min), two Presidential Security Service bodyguards and best friends who were present at the bombing, organize a 21-man team for the mission. However, as the team wreaks havoc in Pyongyang, the five officials abort the plan to avoid an international crisis if the mission is discovered. Their major concern is that the United States will withdraw its nuclear protection if the mission is made public, in light of Seoul's official declaration that it will not retaliate.
The operation is successful, but as the troops swim out from Nampo to an ROK Navy submarine assigned for their extraction, snipers aboard the submarine open fire on them. An already injured Park sacrifices his life to save Lee. Lee swims back to shore and returns to South Korea, where he finds out that the assault team's service and personal records have been erased.
Promising to avenge his fallen comrades, Jin-pyo kidnaps Mu-yeol's infant son, and names him Lee Yoon-sung (Lee Min-ho). He flees to the Golden Triangle to raise the child as his own and trains the boy intensively in combat. Following an attack on a village they are living in, Jin-pyo confesses his long-term plan for revenge to a teenaged Yoon-sung.
Seven years later, after successfully finishing his education and attaining a doctorate in the United States at the Massachusetts Institute of Technology, Yoon-sung returns to South Korea to fulfill his adoptive father's plan for revenge. He enters the Blue House as an IT expert under the National Communication Network Team. He is warned by Jin-pyo not to trust anyone and never fall in love, as doing so will put the people around him in danger.
While working at the Blue House, Lee meets bodyguard Kim Na-na (Park Min-young). Eventually Na-na participates in his revenge plan, as they discover that they have the same goal in mind. Problems occur as Jin-pyo's revenge plot unfolds, especially when Lee defies his surrogate father at several occasions as they try to identify and kill the officials, known as the "Council of Five".
Each member of the Council have achieved significant wealth and political influence since 1983, and are engaged in various levels of corruption. Jin-pyo and Yoon-sung's conflict stems primarily from Jin-pyo's wish to murder each official, and Yoon-sung's wish to teach them a lesson and expose their corruption without killing them. As Yoon-sung exposes the officials' corruption, the citizens of Korea sense an unseen force of justice that they dub "City Hunter".
Council of five, they are cool