A ceremony for the Queen's dethronement is held. She wears all white and her accessories which symbolize her status, are removed. The Joseon citizens are not happy about the dethronement. Meanwhile, Dong Yi is assigned to work in the treasury with the eunuchs. Although it is a difficult job, she keeps working hard. Then, she investigates an issue about the copper shortage and she also notices some mismatch in the book-keeping. This leads her to the money trail that has found its way from the treasury to the team Jang Ok Jeong. She notifies Chief Seo to investigate the matter. 

Dong Yi and Cheon Soo go into town to investigate. But, when Dong Yi is alone for a moment, she is captured by Jang Hee Jae's men. They tie her and later throw her into the river. But, Cheon Soo follows them and manages to save Dong Yi. Although she is still shaken from the incident, she wants to continue the investigation. Unfortunately, Jang Hee Jae has been busy killing all the witnesses. Furthermore, to complicate things, the Queen Dowager dies and Southern Faction pushing hard for the Queen to be removed. Then, by the order of the King, the Queen will be dethroned.

Jang Ok Jeong and her family will be in trouble if they are found guilty of poisoning the Queen Dowager. She then realizes that it is an opportunity to frame the Queen and takes her title. But, both of them are suspects and because the King doesn't know who to believe, he orders Chief Seo to investigate. Jang Ok Jeong's brother wants to kill Dong Yi, in which she refuses at first. But then, when she sees Dong Yi is talking with the King, she accepts her brother's proposal. Then, police finds all the evidence that connect the official who poisons the Queen Dowager to the Queen. Although it is all a set up, the Queen's family and court ladies are arrested and questioned. Meanwhile, Dong Yi and Cheon Soo go out to investigate the matter more thoroughly. 

Jang Ok Jeong notices that it is her brother who plotted the plan to poison the Queen Dowager. She is furious but he says that they have to do this if she wants to be the Queen. This make her realize that she has to change from a kind hearted person into a bad person. Then, Dong Yi also notices that it is Jang Ok Jeong who is behind the poisoning of the Queen Dowager. After that, the King hears that the official who has involved in the poisoning scandal has been arrested. They are all waiting for the confession from the official and it is a shocking confession. The official lies to them and says it is the Queen who asked her to poison the Queen Dowager.

The palace is in confusion with the announcement that Jang Ok Jeong will become a concubine. Western factions are concerned that it will give Namin more power. Then, Jang Ok Jeong becomes pregnant. One year later, Jang Ok Jeong has been promoted to the highest ranking concubine and Southern Faction wants her son to be named Crown Prince. But, Queen Dowager disagrees with the idea. Suddenly, Queen Dowager is seriously ill. Cheon Soo says that if her tonics are mixed with unprescribed herbs, there can be a toxic reaction. Then Dong Yi remembers that she found an unprescribed herb in Jang Ok Jeong's ladies' quarters.

Dong Yi is given three days to find the truth about the Joseon smuggler. She discovers that he staged his own death and the suicide note is not written by him. Then, Chief Seo heads to the nearest port to stop the smuggler from leaving Joseon. Cheon Soo who is given the task of taking smuggler, Kim Yoon Dal to the port, drops him there and watches the police arrest him. Oh Tae Seok is in charge of the investigation decides that smuggler Kim must be punished by death. Jang Ok Jeong sees the King chatting with Dong Yi and she asks him if he has feelings for Dong Yi. He denies it and plans a surprise banquet in Jang Ok Jeong's garden to announce that he will make Jang Ok Jeong his concubine. 

The Qing guards want to arrest Dong Yi for trespassing but the King insists that it will be investigated by the Joseon police. Then, they find out that the code is a name for a place near the river. It is then searched by the police and Chief Seo, who finds the smuggled weapons that belongs to Jang Hee Jae. He is very angry at Dong Yi for finding him out. The King has to talk to Dong Yi now that she knows who he is. Dong Yi begs for forgiveness from the King, who in turns asks her to stay informal like before. Then, Qing wants Dong Yi to be handed to them because of the international incident that she committed before. She then decides to turn herself in.

Jang Hee Jae agrees to help Cheon Soo to find Dong Yi if he works for him. Jang Hee Jae is spooked when he hears that investigators are looking for Cheon Soo. Cheon Soo and Dong Yi run around looking for each other and they finally met. Then, the delegates from Qing have arrived but it's revealed that there are Joseon smugglers in the party. The smugglers are working with Jang Hee Jae and they are prepared to financially support Namin if they can smuggle freely into Joseon. Oh Tae Seok agrees to their demands and he needs to stop the investigations into the smugglers. Dong Yi meanwhile keeps thinking about the paper with Chinese characters on it which is later discovered as a code. Then, she sneaks into the guest house to take the things that she needs and runs away while chasing by the Qing guards. She then rushes over to a man. Then she realizes that the man is the King. 

Dong Yi fails the test. So, she begs her superior for another chance. The Queen is angry when she heard about it and scolds Investigator Yoo because of her behaviour. Then, Dong Yi is given 3 days to prepare for the test and it will be invigilated by Lady Jeong. While she studies for her test, the King turns up to help her. And this time, she passes the test. Meanwhile, the King decides to put Namin instead of the Seoin in power and Jang Ok Jeong will be made concubine. Then, Cheon Soo arrives at the palace as Chief Seo's helper. Even though they work in the palace, they keep missing each other. Young Dal who worries about Cheon Soo, searches his room and finds his Sword Fraternity headband. He takes it to Dong Yi in order to investigate who he is. She is shocked and then rushes to find Cheon Soo. 

The court lady investigators don't want to accept Dong Yi because of her low class origin. But, the Queen who is the head of the inner court refuses to change her decision. Dong Yi arrives at the bureau and gets her new uniform. But, other court ladies are angry with her because they have studied for 10 years to get where they are now and she gets in because of the recommendation from Jang Ok Jeong. Then, she finds out that the investigators are studying for their midterm tests. An evil Investigator Yoo doesn't want Dong Yi in her department. So she tells Dong Yi that she must take the test and not to worry about not knowing anything. But, she does not explain to Dong Yi that she will be expelled from the bureau if she fails the test. 

Dong Yi is saved by the King's guard. She tells him that she has evidence to prove Jang Ok Jeong is innocent. The King and Chief Seo gather in the morgue to watch the procedure again. Unaware of the new development, Queen Dowager and the Investigation Bureau are happy on the downfall of Jang Ok Jeong. Jang Ok Jeong's brother, Jang Hee Jae who is a criminal, arrives from Qing. Then, because of her help, Dong Yi finally gets her reward. She is going to be promoted to court lady in the inner palace and will work in the Investigation Bureau.

Jang Ok Jeong has voluntarily agrees to be investigated. The herbs are found in the Jang Ok Jeong's quarter and she is charged with trying to kill the Queen. But, Dong Yi convinces that Jang Ok Jeong is innocent because the herbs in question are different from the one that she has bought. Then, Oh Tae Seok tries to find a scapegoat to put the blame on and he picks Dong Yi. Meanwhile, Cheun Soo is alive and he gets a job at the city morgue. One night, Dong Yi sneaks into the morgue to check the pharmacist's body for evidence. She finds her evidence and as she sneaks out of the morgue, Chief Seo catches her. So, she tells him about the evidence. On her the way home, she is cornered by assassins but the King turns up. 

The pharmacist who gave Dong Yi the herbs has been murdered. Police interviews Dong Yi, but she says that she gets the medicine for a musician and not Jang Ok Jeong. Chief Seo turns up and when he hears her name, he asks if she is Dong Yi that he knew. But, she says no. The ladies who investigate crimes that are committed by the women are very strict. And they have been ordered to investigate Dong Yi for buying the herbs and illegally bringing it into the palace. Torture tools are being prepared because Dong Yi still refuses to say who sent her to buy the herbs. Then, Jang Ok Jeong arrives just in time to confess that she is the one who ordered the herbs.

Dong Yi wants to take a look at Jang Ok Jeong's personal hanbok accessory as a reward for helping to prove that she is not the cause of the bad omen. Dong Yi is sent to bring medicine into the palace by Jang Ok Jeong's mother. Dong Yi gets back to the palace late and can't sneak in and she is helped to get back into the palace by the King. Jang Ok Jeong refuses to drink the medicine. Then, the word spreads that poisonous herbs have been found in Queen Inhyeon's medicine. Dong Yi goes to pay her respect on the 6th anniversary of her father's and brother's death. On her way back, she gets arrested on suspicion of trying to poison the Queen.

The King keeps saying who he is. Luckily, Chief Seo and his men arrive and save the day. The Queen Dowager devastated to know that her plan has been foiled and the King's life is in danger. And he now knows that someone has changed the music chimes with rock salt. Jang Ok Jeong hands the ID of the corrupt policeman to the Queen Dowager. The Queen Dowager is furious and sees this as a threat. Oh Tae Seok's brother, Oh Tae Poong, who is a new director, comes to the music department and his son takes interest in Dong Yi. He wants her to be beaten up when she refuses him. Luckily, Dong Yi is called by Jang Ok Jeong, who wants to meet her.

Dong Yi manages to escape before she is killed by the bad guy. She finds a policeman but when they go back to the barn, the body is gone. The capital is in turmoil because of the bad omen. The King is determined to find out who is responsible for the musical disaster. But the police and tribunal have come up with nothing. Dong Yi decides to do the investigating herself. She takes evidence dropped by the bad guy and then goes back to the barn, where the King turns up. Then, there's an argument outside the barn and the King bumps into Dong Yi when he hides. They escape together and as the collect more evidence, they get cornered by armed men. 

Six years have gone by and Dong Yi is now a young woman. Then, a meteorite is landed in the palace, a bad omen. Jang Ok Jeong's protesters blame this on her. Furthermore, the Western Faction is stronger than the Southern. Jang Ok Jeong is supported by Southern Faction, but the Western Faction is supported by the Queen Dowager and Oh Tae Seok. They do not like her and plan a 'bad omen'. Later at the banquet, the orchestra can't play in tune and says that it is a bad omen. Dong Yi tries to find the lady with the butterfly accessory. But, she is found loitering around and she is arrested and tied up in a barn with a dead man with the chimes earlier.

Chief Seo orders the city to be searched for members of Sword Fraternity. Dong Yi is still on the wanted list. So, when she takes her friend, Gae Doo La to the hospital, she is arrested by Chief Seo. Luckily, he lets her go and tells her about the hand signals. Dong Yi asks her brother's friend, Seol Hee to get her into the palace as a servant because she wants to find out what happened to her father. Meanwhile, a girl's body is found and Chief Seo confirms it although it is not her. Dong Yi enters the palace and starts working in the music department. She starts to play a sorrowful tune using a daegeum, which reminds her of her brother and father. Many years later and it's now the 19th year of King Sukjong and Dong Yi is now a young woman.

Dong Yi's father and brother are taken into custody. Dong Yi is taken to a fortune teller's place. He predicts she will be the leader of Sword Fraternity. Oh Tae Seok announces that Dong Yi's father and brother will be executed the next day. Some evidence has been found in the Sword Fraternity headquarters to prove that they are guilty. Cheun Soo and members of Sword Fraternity make plans to free Dong Yi's father and brother. Dong Yi sees a young aristocrat lady do the same hand signal that the dying official has showed at the riverside. The escape plan works, but they get chased and killed. Dong Yi hears that her father has escaped and runs to find her. But, she only sees corpses and the embroidered purse she has given to her father.

Oh Tae Seok wants to frame Sword Fraternity for the murders of Southern Faction and the police officer. Chief Seo asks his father to speak to the king about opening the investigation again. But, King Sukjong is at his father's grave. So, Chief Seo's father goes to visit him there. The Sword Fraternity realise that Oh Tae Seok is planning something. They rush to stop it, but all of them are dead. The corrupt police tries to frame them, but they manage to escape. Meanwhile, Dong Yi finds herself in a noble lady's house. Dong Yi prepares to do the greeting, but her father refuses to let her go. But Dong Yi sneaks away. She has to greet Oh Tae Seok. He then realises who she is and ask his men to kill her. But, Cheun Soo saves her. Then, a member of Sword Fraternity betrays them and leads to the arrest of Dong Yi's father and brother.

The story begins in 1681, 7th year of King Sukjong. Dong Yi lives with her father and brother in a slave village. They are the members of Sword Fraternity, which is the organisation made up of the lowest class people. Then, a high ranking government officer from Southern Faction was assassinated. After that, Dong Yi finds the assassin ID and hand it to the police. But, it belongs to a corrupt policeman who worked for Oh Tae Seok. He is arrested, but gets killed in his prison cell. Dong Yi's father has the information, so Oh Tae Seok's masked man try to kill him but he gets saved by his friend, Cheon Soo. When they get home, Dong Yi is not there.