The historical drama takes place in the twilight years of Goguryeo. Military general Yeon Gaesomun wants to go to war with the Tang Dynasty, but the pacifist King Yeongnyu opts for diplomacy and national stability, and in their battle of wills the palace council is divided between the "hawks" and the "doves."
Yeongnyu has two children, the princess So-hee, and the crown prince Hwangwon. The king is particularly proud of his older daughter So-hee for being intelligent, assertive, empathetic, and an excellent swordswoman, and he respects her opinion during their frequent discussions about matters of state and politics. Despite being the heir, the younger, more frail Hwangwon acknowledges that he isn't particularly suited to rule, and prefers to quietly read his books in his quarters. Nevertheless, the siblings share a close, loving relationship with each other and their father.
Meanwhile, hoping for an audience with his father, Yeon Gaesomun's illegitimate son Choong arrives in the capital after the death of his mother, a former slave. While on the road, the crown prince and princess are attacked in their carriage; Yeon Gaesomun and his allies had hired assassins to fake a Tang attack, since this could become grounds for war. Observing this from a rooftop, the masked Choong uses his bow and arrow to kill the one surviving assassin in custody, to prevent him from implicating his father. Shortly after, Choong and So-hee meet in the marketplace and fall in love at first sight.
After his father rejects him, Choong decides to make something of his life and becomes a member of the royal guard, with So-hee ignorant of his paternity. When he foils another assassination attempt, Choong gets recognized by the king's nephew Jang as the masked archer, and he is sentenced to death. Yeon Gaesomun preys on Jang's ambitions, and together they plot to save Choong from hanging, unbeknownst to the grieving So-hee, who believes he has died. But Choong cannot resist revealing himself to her, and the lovers joyfully reunite.
Fearing that the general's power and influence are rapidly overtaking the throne's, Yeongnyu orders Yeon Gaesomun to oversee the construction of the defensive wall Cheolli Jangseong in a remote province, which would effectively exile him. In retaliation, Yeon Gaesomun and his co-conspirators plan a revolt; it fails because of Choong's intervention, but the crown prince becomes seriously injured after he falls off a poisoned horse. The king unexpectedly declares So-hee as his successor to the throne, dashing Jang's hopes and causing him to finally shift his allegiance to Yeon Gaesomun.
Yeongnyu asks the Geumhwadan, a secret group of warriors meant to protect the royal family and the citizens in times of uprising and war, to investigate. But they have difficulty finding unequivocal evidence linking Yeon Gaesomun to the failed rebellion. Seeing no other solution to their ideological impasse which is causing political unrest, Yeongnyu decides to have the general and his fellow traitors assassinated. But Yeon Gaesomun has his own carefully laid plans in place, and he warns Choong to correctly choose a side, with his family. He tells Choong to cut off the princess's head to prove his loyalty, and orders a soldier to kill Choong if he acts against them. Enormously conflicted yet unable to betray his father, Choong agrees to join the plot, but only because he's secretly planning to save So-hee from what's to come.
Thus, Yeon Gaesomun, his allies and their troops enter the palace, launching a bloody coup. The royal army stands down under Jang's orders, and the plotters massacre the ministers in the council and the remaining loyal soldiers. So-hee's brother the crown prince is murdered in front of her eyes. The Geumhwadan urge the king to escape, but he stands his ground in the throne room, facing his enemies with dignity. Truly believing that he is doing what's best for Goguryeo, Yeon Gaesomun commits regicide by stabbing Yeongnyu straight through the gut with his sword. Once she sees Choong there, the utterly devastated So-hee assumes the worst that he was part of the conspiracy, not realizing that Choong risked his life fighting his father's own soldiers to protect her.
Yeon Gaesomun installs Jang as the new king Bojang. But he is only a puppet king, and Yeon Gaesomun becomes the de facto ruler and dictator of Goguryeo. Believing that So-hee had died, Choong reverses his earlier stance and joins Yeon Gaesomun's cause in order to gain power, castigating himself that if only he hadn't been powerless, he might've been able to save her. But So-hee is alive, and being hidden by the Geumhwadan. She renames herself Moo-young (meaning "shadowless" because she no longer exists in the world), and vows to avenge the death of her family.