As Royal Secret Agent draws its curtains close, Sung Yi-gyum (Kim Myung-soo) and Park Chun-sam (Lee Yi-kyung) face an ambush and are unable to reach the provincial guards. They are brought to the provincial office, where a beat-up Kang Soon-ae (Jo Soo-min) is waiting. The final episode of the show recorded 10.2 and 14 percent ratings.
Hong Da-in uncovers a revolt
On their way back to Hanyang, Hong Da-in (Kwon Na-ra) and Choi Do-gwan (Shin Ji-hoon) stop to eat. Da-in overhears whispers of a coup led by Sung Yi-beom (Lee Tae-hwan). She convinces Do-gwan to head back to Jeonju and notify Yi-gyum of the upcoming coup. Meanwhile, in order to take back the provincial office, Yi-beom recruits people for a revolt. Many who are indebted to Jeon Gye-su (Park Dong-bin) join, and Yi-beom proceeds with the revolt.
Sung Yi-gyum learns the truth
At the provincial office, Hak-su reveals why Yi-beom and Soon-ae had to flee their old town—Soon-ae is Catholic, which is a punishable crime. Yi-gyum remembers Yi-beom’s promise to look after Soon-ae while his older brother is gone and finally understands why Yi-beom had to take a different path. Hak-su orders them to be imprisoned, then goes to Kim Byeong-geun (Son Byung-ho), who forges a letter to the King (Hwang Dong-joo), falsely accusing Yi-gyum of starting a revolt with his brother Yi-beom.
Sung Yi-beom fails at the coup
The captain of the provincial guards can no longer stand Hak-su’s cruelty and decides to side with the royal secret agent and free him. Meanwhile, Hak-su learns of the captain’s betrayal and lays out a trap for Yi-gyum at the provincial office. Yi-beom and his men arrive earlier than Yi-gyum and are caught in the trap, rendering the coup unsuccessful. The following morning, Yi-gyum leads the station guards to free everyone at the slave market. He proceeds to the office and finds a badly wounded Yi-beom and his men tied up. Hak-su and Byeong-geun appear and tell everyone that Yi-gyum has conspired with Yi-beom.
Sung Yi-gyum is his brother’s keeper
Byeong-geun tells Yi-gyum that the only way to clear his name is if he executes Yi-beom himself. Yi-gyum picks up a sword and tells Yi-beom how cruel fate is to have given them such an unfortunate end. He then lowers his sword and says he can never harm his younger brother. Just as he loses hope, Da-in and Do-gwan arrive with many more station guards and apprehend Hak-su and Byeong-geun. As one last desperate attempt to take revenge, Byeong-geun charges at an unaware Yi-gyum with a dagger. Yi-beom runs to protect his brother and is stabbed in the chest. Horrified, Yi-gyum catches him, and with his last words, Yi-beom apologizes to Yi-gyum before falling into his comrades’ arms.
Sung Yi-gyum gives Park Chun-sam his freedom
On their way back to Hanyang, Yi-gyum secretly meets with Soon-ae, who leads him to Yi-beom who is still alive. His fake death turns out to be Yi-gyum’s ploy to escape punishment, as a revolution is still a punishable crime. With the assurance that his brother is alive and Soon-ae is safe, Yi-gyum sends them off with a blissful heart. In Hanyang, Hak-su is sentenced to exile, while Byeong-geun is executed. Yi-gyum believes Chun-sam has served him well his whole life, and to reward him for his loyalty and service, he grants Chun-sam his freedom.
The royal secret agent goes on his last mission
Word has reached the Palace that several men are impersonating Yi-gyum to extort money from officials. Yi-gyum has no choice but to go out again as a royal secret agent. At the gate, he stumbles upon Chun-sam, now a free man, who decides he shall remain as Yi-gyum’s entourage in his mission. Da-in also joins them, but she has Yi-gyum promise that after this mission, they will settle down in Hanyang. Together, they set out for their last mission.