Three years after the assassination of Hyun-Jun, IRIS is attempting to break Baek San out of NSS prison. The NSS assigns it's new recruits to guard Baek San.
Yoo-Gun plans to use Baek San as bait to figure out what IRIS wants with him and who the IRIS mole is in the NSS base. Soo-Yeon tries to recover from the effects of killing for the first time.
Yoo-Gun is living in Japan with amnesia. IRIS has manipulated him into working for them, as an assassin. Meanwhile, the NSS follows Park Cheol-Young to Japan, believing him to be a member of IRIS.
After killing Park Cheol-Yeong, Joong-Won returns to the North as a hero. The NSS prepares for an attack, from Yoo-Gun and IRIS, at the North and South reunification meeting.
The North and IRIS have staged a kidnapping of a Northern Representative and are blaming it on the South. Now, the NSS has 24 hours to find the terrorists or it'll be war.
IRIS plans to exchange Yoo-Gun for Baek-San. But, the NSS believes that Yoo-Gun is now a member of IRIS. Soo-Yeon finds out that Baek San is really Yoo-Gun's father.
Choi-Min decides to work with Yoo-Gun, secretly. Ray and Soo-Jin negotiate with the NSS, offering to hand over Mr. Black for their freedom. Yoo-Gun finally finds out that Baek-San is his father.
Yoo-Gun pursues Joong-Won for killing his mother. Soo-Yeon mopes over her brother's death. Beak-San reveals the location of the nuclear bombs to Choi-Min.
Hyeon-Kyu has discovered that the bullet piece, inside Yoo-Gun's head, may turn him into a psychotic killer. Yoo-Gun captures Yeon-Hwa. There is a new spy in the NSS.
The NSS interrogates Hyun-Woo and Shi-Hyuk to see which one is the spy. Cheol-Hwan returns to the NSS. Joong-Won captures Soo-Yeon and plans to use her as bait for Yoo-Gun and Baek-San.
Mr. Black sets up a meeting with Joong-Won. Yoo-Gun gives Baek-San's hard drive to his allies at the NSS. Choi-Min is relieved of her position at the NSS for trying to transport the nuclear bombs to the U.S without authorization.