Best friends Kim Hyun-Jun (Lee Byung-hun) and Jin Sa-Woo (Jung Joon-ho), were training under the South Korean army's 707th Special Mission Battalion until they were scouted by NSS (National Security Service). The duo was independently scouted by the beautiful NSS agent, Choi Seung-Hee (Kim Tae-hee); the two didn't realize they have fallen for the same woman and continued to win her love. Unaware they have been scouted, the two were secretly captured and subjected through a simulated torture test and the duo passed their test to be worthy NSS agents.

After completing the test, Hyun-Jun and Sa-Woo were introduced to the director of NSS, Baek-San (Kim Yeong-cheol). Baek-San explained to them that the NSS is a secret organization tasked with preempting foreign threats and protecting the country's interests through wetwork operations, including assassination of anyone who could be a threat to South Korean (SK) national security. Since its founding in 1976, during the rule of Park Chung-hee, the agency's very existence has remained a state secret from everyone, including the President.

After entering NSS, the pair learned that Seung-Hee was their undercover scout agent. While the duo was surprised and somewhat hurt, Hyun-Jun was angered the most as he felt his heart was toyed with; during a team celebration dinner, Hyun-Jun confronted her alone and the two embraced the passion they have for one another. Afterwards, the two maintained a secret romantic relationship without the knowledge of anyone.

Hyun-Jun and Seung-Hee took the opportunity to secretly fly off to Akita-Japan for a romantic winter escape after saving the life of SK President Cho Myung-Ho (Lee Jung-gil); Baek-San seized opportunity to reveal NSS to the president to gain his support. While vacationing, the couple befriended a young teen, Yuki (who was smitten with Hyun-Jun at first sight). However, their vacation was cut short after being recalled back by NSS for a life-changing mission at Budapest: recovering the head NK nuclear scientist, Hong Seung-Ryong.

At Budapest, Sa-Woo catches up with Hyun-Jun and Seung-Hee to extract Hong Seung-Ryong back to SK; Sa-Woo learned of their romantic relationship and pretended to be happy for them. Unfortunately, Hong Seung-Ryon was killed along with his handlers by IRIS Agent, Vic. Afterwards, Baek-San (who is secretly an IRIS agent) tricked Hyun-Jun by having him assassinate North Korean Minister Yoon.

Hyun-Jun successfully killed NK Minister Yoon and was on the run. NK agents, Seon-Hwa and Cheol-Young, hunted for Hyun-Jun as he escaped. Wounded, Hyun-Jun escaped capture and tried to get help, but Baek-San betrayed him by manipulating Sa-Woo to silence him; he escaped capture and ater reunited with Seung-Hee. The couple agreed to run away together, but both thought each other had been killed by the enemy (Seung-Hee by car bomb and Hyun-Jun by crashed plane). Because of their failure to capture Hyun-Jun, NK agent, Seon-Hwa, was stripped of her title and jailed.

Both Hyun-jun and Seung-hee survived their ordeal. Hyun-Jun was rescued by Jeong-Hoon (a friend of Hyun Jun's deceased parents and revealed Baek-San murdered them). Seung-Hee refused to accept Hyun-Jun's death, but Sa-Woo convinced her he is dead. Jeong-Hoon warned Hyun-Jun of a war profiteering organization known as IRIS, a force that had long existed to create political turmoil to profit from a country's strife and his counter-agency that opposes them. Not willing to help a stranger, he escaped to Akita-Japan to investigate.

NK intelligence later found out Hyun-Jun lives and gave Seon-hwa a final chance to kill Hyun-Jun for redemption. Seon-Haw failed and was captured by Hyun-Jun; he gave mercy and even offered his life to her after he completes his quest for vengeance. Seon-Hwa believed him and eventually integrated herself with Yuki's family as well. Over time, Seon-hwa falls in love with him. The two eventually make their way back to Korea after an unfortunate scuffle with Vic that lead to Yuki and her family's death. Hyun-Jun defects and cooperates with a NK black-ops team to get his revenge on Baek-San.

Not long, Baek San and Sa-Woo (manipulated into working for IRIS) found Jeong-Hoon. They used NSS resources to track him down. Before Jeong Hoon died, he activated a video feed to record his final moments for Hyun-Jun (via cell phone video) to see. The video was meant to be part evidence and also a clue for Hyun-Jun to continue his mission; the clue led him to meet President Cho Myung-Ho once again. In a private meeting, Hyun-Jun finally had a chance to explain his side of the story and that he is now a double-agent between both sides to stop a nuclear plot (by IRIS) from happening.

Around the same time, Cheol-young, discovered his own commanding officer, Gi Hoon, is part of a coup with IRIS to start a civil war and take control both sides of Korea under their unified control. Hyun-Jun and Seon-Hwa teams up with the very black-ops team that's in charge of nuking South Korea. Because he's not trusted, Hyun-Jun helped the team infiltrate and attack NSS HQ to steal special equipment to complete building their nuke. However, their actions wasn't enough to earn the team's trust as they had their own agendas and the team went ahead with their plans without Hyun-Hun and Seon-Hwa.

It was between this time that Hyun-Jun finally reunited with Seung-Hee and learned what really happened at Budapest, including Sa-Woo's actions. It was also the first time she learned about IRIS, however, there wasn't enough time to explain things as NSS agents are after them. Seung-Hee confronts Sa-Woo with the truth and told him she'll never forgive his actions against Hyun-Jun.

Impatient of allowing IRIS to act any further through NSS, President Cho Myung-Ho had Head of National Security, Yoo Kwang-Ho, execute a hostile takeover on NSS; both Sa-Woo and Baek-San were arrested for conspiracy. Later, on the president's official announcement of reunification, Hyun-Jun and Seon-Hwa searched for the hidden nuke. During this time, Cheol-Young successfully rooted out IRIS agents within North Korean ranks; through arrested confessions, he reported to the duo that IRIS had targeted the Federal Building Complex, the U.S. Embassy, and the Blue House. While searching throughout Seoul, Hyun-Jun realized the notes they found earlier corresponded to a particular bus route and figured out the nuke was within a moving tour bus. However, their former NK black-ops teammates tried to stop them in a massive gunfight to lead to their deaths; Hyun-Jun saved the day. With the nuke neutralized and all enemy forces killed, the SK president thanked Hyun-Jun in his efforts and earned his complete faith.

Peace had finally come and Hyun-Jun took time off. Afterwards, Hyun-Jun took the time to bid farewell to Seon-Hwa. Even though Hyun-Jun got presidential permission to allow Seon-Hwa live in SK; due to her unrequited love for Hyun-Jun, she declined and returned to NK. Seon-Hwa wanted to retire from being an agent; she would quickly return to SK with the Cheol-Young when she realized Seung-Hee's profile was within a discovered IRIS personnel database and wanted to warn Hyun-Jun of the potential danger.

Meanwhile, Hyun-Jun went to Jeju Island to vacation with Seung-Hee, but inexplicably left without notice. Hyun-Jun couldn't find her as he was called back to Seoul due to the IRIS jailbreak with Sa-Woo and Baek-San. She would later confess that she met with Baek-San as he tried to recruit her into IRIS. She explained that Baek-San helped raise her like a daughter and she didn't want to talk about it due to personal conflicts within herself; Hyun-Jun sympathized and forgave her.

In the hunt for Baek-San, Hyun-Jun found and killed Vic; he avenged Yuki's death. Clues left behind suggests that IRIS had hidden themselves within private golf club house; Hyun-Jun infiltrated and attacked the golf club house with an NSS team to arrest Baek-San and Sa-Woo, but Sa-Woo escaped. When Hyun-Jun and Baek-San finally meet, Hyun-Jun demanded Baek-San to ask for forgiveness, but Baek-San couldn't help laugh at the matter. Hyun-Jun was tempted to kill Baek-San, but Hyu-Jun had him arrested.

Later, Sa-Woo and IRIS agents attacked a local mall for hostages to blackmail both sides of the Korean government to release their IRIS agents and to make SK's president announce their political stand to not unite with NK. Hyun-Jun became the negotiator for the president and for the hostages' release, but he was really there to appeal to Sa-Woo's conscience. Because the IRIS agents had conflicting commands with Sa-Woo, Hyun-Jun and Sa-Woo were forced to team up again and kill all the IRIS agents. During the gun-fight, Sa-Woo was mortally wounded. Dying before his friends, he apologized and was forgiven before he passed away. With all things hindering the reunification process gone, the peace talks resumed.

At the reunification summit, the president personally requested Hyun-Jun to be at his side. Concurrently, NSS agents realized they've been duped: the presumed dead IRIS agents at the mall crisis was actually the hostages. The true IRIS agents escaped and infiltrated the summit to kill all delegates. IRIS agents killed and replaced various security agents for a massacre. Unfortunately, it failed with Seung-Hee's interference. She pretended to be an IRIS agent and used the confusion to stop them. This created mass panic as IRIS agents make their stand against all security forces. Ultimately, the SK president and NK forces survived the assault and Hyun-Jun saved the day again.

In the aftermath, Hyun-Jun and Seung-Hee left NSS for a normal life. While Seung-Hee waited at a lighthouse for Hyun-Jun, he was driving up to meet her and propose. However, during the drive, Hyun-Jun was sniped in the head by IRIS Agent Ray (from IRIS II). Afterwards, Hyun-Jun’s life and death were later classified, Baek-San was sent to a “black prison,” and IRIS receded for three years until they regained their strength to take on the world once again.