The story explores the origins of the former Director of the NSS and IRIS agent, Baek San (Kim Yeong-cheol), and the protagonist Jung Yoo-gun (Jang Hyuk).

Her life is destroyed after the North Korean dictator decides to crack down on people he considered traitors to the country, resulting in the death of her daughter and husband.

Yoo-gun will be raised on a farm with his mother, occasionally being watched over by a detective (due to his rebellious upbringing) and eventually starts a long-term relationship with his childhood sweetheart, Ji Soo-yeon (Lee Da-hae).

During a prison transfer gone horrifically wrong, Soo-jin tips off Ray and IRIS kills all NSS agents in one of their secret camp locations.

IRIS nearly manages Yoo-gun's capture if it weren't for him intentionally driving into a Korean Army base and requesting assistance.

Baek San feels indebted to Yoo-gun and decides to tip him off about IRIS's next scheme: disrupting the reunification plans between North and South Korea.

Baek San also warns Yoo-gun that IRIS is playing a dangerous game and details of their intent are unclear as their targets could be against the north and/or south.

Meanwhile, Yeon-hwa accepts a mission from IRIS, but requires the aid of another rogue North Korean asset to complete the job.

She travels to Cambodia to recruit Yoo Joong-won (Lee Beom-soo) to help her assassinate the head minister of the reunification plans on North Korea's side to disrupt peace talks.

Yoon-gun and his team are to be the security detail to the former South Korean President Cho Myung-ho (Lee Jung-gil) as he leads negotiations with North Korea.

Yeon-hwa kills a Chinese servant, Mei, and takes on her identity to gain access to the hotel where the delegates are staying.

Prior to the incident, both NSS and North Korean agent Park Cheol-yeong (Kim Seung-woo) suspect that something about Mei is wrong.

The North Korean security detail tries to arrest Yeon-hwa, but Joong-won provides long range coverfire to insure her escape.

With the cooperation of Choi-min, Yoo-gun intentionally orchestrates a false prison transfer of Baek San to lure the infiltrator as well as baiting IRIS out into the open in order to trap them.

As expected, the lure tactic unfolds as planned and Lee Soo-jin informs Ray to attack the transport team in attempts to extract Baek San.

In the ensuing chaos of the gun battle, IRIS agents extract Ray's surviving team as well as taking the dying Yoo-gun with them as insurance.

In the aftermath, Lee Soo-jin is arrested after being discovered that she copied the security director's ID card to gain unauthorized access to NSS servers.

When Soo-yeon shoots Soo-jin, Choi-min sympathizes with her personal situation (as she has lived through something similar in the past), protecting her at risk of her own position.

While staying at an inn in Akita-Japan, IRIS agent Rie and her father act as his minder to make sure his old memories don't resurface to cause complications; but the rouse cannot last forever.

She eventually finds the engagement ring he has kept hidden in a doll during the mission in Budapest and she wears it as a sign and statement of her love for and faith in Yoo-gun.

Joong-won, himself, pretends to be part of the security details for the general's safety, but it is but an elaborate ruse to stimulate talks of war between the North and the South.

Yoo-gun successfully infiltrates the secret housing location of where the North Korean general is hiding and aids in "kidnapping" him, thus giving Joong-won the excuse to declare the incident as an act of war, proving he isn't afraid of launching using nukes by priming their missiles.

During the chaos, Baek San escapes and Yoo-gun returns to NSS custody to be debriefed and considered to be an untrustworthy asset.

Through a doctor's exam, it has been revealed that the bullet is still inside Yoo-gun's head and is causing him to experience headaches, random acts of rage, loss of emotional control, and likely will kill him over time.

Commander Choi-min later secretly rehires Yoo-gun, believing he's the best chance of finding IRIS; turning it into a black-ops mission.

He turns over two of the nukes to the NSS and Choi-min informs the president of their incredible find, creating a new window of questionable opportunity.

Partially to gain international recognition and also to show that they can hold their own and threaten North Korea in equal measure and capacity.

Priming the nuke to destroy the city, he is stopped with the help of Yeon-hwa and dies during a gun fight between NSS agents.

[28] According to AGB Nielsen Media Research, the premiere episode achieved a nationwide rating of 14.4 percent in viewership, ranked first ahead of 7th Grade Civil Servant on MBC and That Winter, the Wind Blows on SBS.

[31][32] In its third week, That Winter remained on top, while its Iris competed for second place with small differences in viewership rating with Civil Servant.