The story begins around the same time as Iris, when Kim Hyun-jun is being hunted down by North Korean agents and branded a traitor while in Budapest. South Korean President Cho Myung-ho (Lee Jung-gil) expressed interest in advancing nuclear technology to lead the world with the most advanced and cost effective energy source of the century. To do this, he enlisted black-ops agent Dr. Kwon Yong-kwan (Yoo Dong-geun) to help retrieve a defecting North Korean scientist, Dr. Kim Myeong-guk.
Dr. Kwon accepted the mission, but it was nearly ruined by an Athena team, led by Son Hyeok (Cha Seung-won). Ultimately, Dr. Kwon managed to secured Dr. Kim's retrieval, but he was caught himself by Son Hyeok and tortured for information. Son Hyeok was supposed to kill Dr. Kwon, but he let him live out of momentary mercy. Three years after those events, President Cho re-enlisted Dr. Kwon to serve as the director of the new counter-terrorism task force, NTS (National Anti-Terror Service), to protect South Korea's future from aggressive foreign enemies trying to steal Dr. Kim's nuclear technology.
After Dr. Kwon arrived to be part of NTS, his old rival, Son Hyeok, had returned to South Korea as the new director of DIS (an American intelligence agency). At the same time, SK NIS (National Intelligence Service) agent Lee Jung-woo (Jung Woo-sung) recently transferred to NTS to become their top agent. Unknown to everyone, Son Hyeok is a double-agent between DIS and Athena, an organization of influential people that controls the world's resources for their fortunes. With the help of another Athena double-agent, Yoon Hye-in (Soo Ae), she infiltrated NTS and supplied Son-Hyeok with inside information about their activities. In a major grab for Dr. Kim's technology, both NTS and Athena had thwarted and countered each other in a high-stakes game of controlling the next great power resource.
Willing to do anything to gain the upper-hand for Athena, Son Hyeok had President Cho's daughter, Soo-young (Lee Bo-young), kidnapped in Italy and used her as ransom to gain Dr. Kim. However, Jung-woo rescued Soo-young. To throw off Athena, Jung-woo helped fake Dr. Kim's death to prevent them from trying any further, but that deception was exposed. Athena recovered Dr. Kim and forced him to complete his project for Athena instead.
NTS later found out Dr. Kim was kept in a secret facility in Japan. To avoid making their intel known, Jung-woo was dispatched under false pretenses as a body guard for pop star, BoA, to make it seem their cover wasn't exposed. In NTS's quest to find Dr. Kim, they failed to rescue him, but NTS managed to recover a crucial component to Dr. Kim's technology and Athena wants it back. Using Jung-woo's feelings for Hye-In against him, Athena faked a hostage situation that blackmailed Jung-woo to return the component for Hye-in. However, that was thwarted as well, but at the price of Dr. Kim's life.
Fortunately, Dr. Kim managed to complete enough of his work that other scientists could complete it without him. Before he died though, he also secretly left a code that revealed North Korea's full nuclear capabilities; it prompted President Cho to speed-up peace negotiations between North Korea, but it was a rough process as North Korea found out they harbored Dr. Kim and they intervened against both sides. During this time, all the things Hye-In had done for Athena created a crisis of loyalty and ethics for Hye-in. She is loyal to Son Hyeok, but also developed feelings for Jung-woo. With Athena's new goal of destroying the nuclear project before completion, Hye-in struggles to balance between orders from Athena and keeping Jung-woo alive.
After Son Hyeok's Athena affiliations was exposed, he was arrested by NTS for questioning. However, Athena agents recovered him and he's now planning to kill President Cho. During this time, Jung-woo figured out Hye-in is an agent for Athena, but due to his love for her, he allowed her to escape NTS. However, because of her activities related to Son Hyeok, she was implicated along with his actions. Because Athena questions Hye-in's loyalties, she was confined, but she managed to inform Jung-woo of President Cho's impending danger. Later Hye-in gets arrested is and held inside NTS. She eventually chose to defect from Athena and aided NTS to stop Son Hyeok.
With so many failures, Son Hyeok was stripped of his rank in Athena and his men replaced with a new team. Athena is aware of the problems Hye-in caused; she was also marked for death. Unwilling to allow Hye-in to die, Son Hyeok and his team killed their replacements and gone rogue. Driven by his hatred, he sees NTS (especially Jung-woo) as destroyers of his ambitions for power and taking away Hye-in; he used all his abilities to destroy them all.
In a final endgame mission, Son Hyeok and his rogue team infiltrated NTS. They disabled the facility using an EMP device and tried to kill as many NTS agents as possible. Although many NTS agents were killed, Jung-woo, Director Kwon, and Hye-in managed to defeat them. In a showdown between Son Hyeok and Jung-woo, Jung-woo was proven the better fighter, but Son Hyeok stopped him at gun point. Hye-in intervened to stop Son Hyeok, but he couldn't stop. Therefore, Hye-in shoots Son Hyeok. Hye-in tried to kill herself to end the madness, but Son Hyeok wanted her to live. Soon, Son Hyeok died while Hye-in survives. After recovering from her injuries, Hye-in was given amnesty and she left South Korea. One year later, Jung-woo left NTS to be with Hye-in in New Zealand. He found and surprised her in Auckland, where he hopes to start a happy chapter with her. The drama ends with the main couple smiling at each other.