The story takes place in Seoul, 2011. Lee Yoon-sung is a talented MIT-graduate who's working on the international communications team at the Blue House. He encounters dangerous situations while solving a variety of cases, both big and small, for people who need his help, and eventually becomes a "city hunter."
After his entire unit is betrayed by their country, Jin-pyo decides to raise his late friend's son up, as a warrior, in order to get revenge on the five politicians that were in charge of his unit's mission.
Yun-seong goes under cover, as a doctor for the Blue House, in order to get close to his first target, Senator Lee Kyung-wan. Kim Na-na gets a job as a bodyguard to the president's daughter.
Yun-seong tries to gather enough evidence to expose Kyung-wan's true colors.
Jin-pyo decides to take his revenge into his own hands. Now he and Yun-seong are in a race to catch the rest of the politicians.
The next target is the Minister of Defense, Seo Yong-hak, who is in favor to win the presidential election. In the meantime, Yun-seong tries to mend his relationship with Na-na.
Yun-seong and Na-na move in together so that he can protect her. Yun-seong and Sik-Joong try to gather enough evidence to take Yong-hak down.
Yun-seong and Shin-joong plan to expose that Yong-hak's sons' illnesses are fake, so that they'll join the army. Yun-seong finally agrees to tutor Da-hye.
Yun-seong tries to make sure Na-na isn't around for when he tries to take down Yong-hak again.
Yun-seong and Jin-pyo's next target is Kim Jong-sik, the former Minister of Education and Young-joo's father. Yun-seong tries to cut himself out of Na-na's life in order to protect her.
Young-joo believes that Yun-seong is the City Hunter, but he can't prove it. Na-na tries to deal with the knowledge of knowing Yun-seong is the City Hunter and her feelings for him. Kyung-hee finds out that she has leukemia.
Yun-seong quits his job at the Blue House in order to cut himself out of Na-na's life. Jin-pyo plans to use Yun-seong's mother as a hostage in order to keep Yun-seong under control.
Na-na offers to help Yun-seong take down the rest of the politicians. Young-joo tries to persuade his father to come clean with the money that he's stealing from the college.
Young-joo has been taken off the City Hunter case, be he rufes to give up. Shik-joong searches for Yun-seong's mother. Yun-seong and Na-na try to gather the proof that will take Jong-sik down.
Tensions grow higher between Yun-seong and Jin-pyo. Kyung-hee finally finds out that Yun-seong is her long lost son. The next target is Haewon Group president Chun Jae-man.
There have been complaints from employees working at Haewon Group's company about working with toxins. Kyung-hee receives Yun-seong's bone morrow. Young-joo investigates Yun-seong's background.
Yun-seong tries to cut himself out of Na-na's life, once again. Jae-min is growing desprate to keep his employees under control.
Jae-min is on to Jin-pyo. Na-na has been assigned to protect the president. Yun-seong tries his best to get over Na-na. Young-joo is back on the City Hunter case.
Yun-seong tries to carry out Jin-pyo's plan. Jae-min starts making desperate moves to save Haewon from going into bankruptcy. Young-joo tries to catch Jae-min before the City Hunter does.
Young-joo now knows that Yun-seong is the City Hunter. Jae-min escapes. Yun-seong learns a long kept secret about his father.
Yun-seong and Jin-pyo's fifth and final target is Choi Eung-chan, the South Korean President.
