Dr. Kim Myung Guk has been missing for three years. Ever since a terrorist organization tried to capture him for his development on nuclear weapons. But now, the National Anti-Terror Service (NTS) has information that the organization has found him.
Lee Jung-Woo is on temporary leave from NTS. He heads to Japan to solve a missing clue that Dr. Kim Myung Guk left behind before his death. Son-Hyeok orders Hye-In to follow Jung-Woo and kill him. But will Hye-In's feelings get in the way?
Son-Hyeok has been brought to NTS for interrogation. Jung-Woo, Jae-Hee, and Joon Ho are in charge of it. Some of the evidence they find leads Jung-Woo to believe that Hye-In may be a member of Athena.
Jung-Woo confronts Hye-In about being part of Athena but, out of love for her, he lets her go on the run. Meanwhile, there is evidence of a spy in the Blue House. NTS finds out the it's Han Jung Pil, Jae-Hee's father.
Dr. Kim Myung Guk has been kidnapped and the NTS have no leads on his whereabouts. Meanwhile, Jung-Woo and Jae-Hee are sent to Japan to protect Korean pop star, BoA, from a terrorist threat.
The SNC has been recovered. But now, Athena wants it back. They force Jung-Woo to get it back for them while holding Hye-In hostage. With Ki-Soo's help, Jung-Woo recovers the SNC and kills the terrorists. But his career with the NTS could be in jeopardy.
Jung-Woo believes that Hye-In was the sniper that killed Han Jung Pil and he holds himself responsible for how his death has effected Jae-Hee. Meanwhile Athena prepares for an attack on the President before his meeting with Saudi Arabia.
The NTS finds out that Dr. Kim Myung Guk and the stolen SNC are both in Japan. Now they have to locate their exact location. Joon Ho sees this as his chance to rediscover his combat agent skills.