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.

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.

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 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.

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.

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.

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.

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.

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.

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.

The eunuchs refuse to let the lady investigators do the audit. Then, the King decides that they shouldn't continue with the audit because he wants to investigate the copper shortage secretly. Dong Yi visits the Queen to assure her that they can find the proof of her innocence soon. When the King goes to visit his parent's grave, he brings most of the guards with him. Because of that, the palace is quite and Jang Ok Jeong with her brother decides to set the treasury on fire. They also send assassins to kill Dong Yi, but she is not in her bed. Dong Yi is in the treasury looking for the record books when the fire starts. She run away and chased by the assassins.

Jang Hee Jae arrives at the city to bribe the delegates from Qing. Sir Shim, an exiled nobleman who stays with the merchant is suspicious about Jang Hee Jae. So, he becomes the interpreter at the meeting and soon discovers that Jang Hee Jae intends to give the records of Joseon's national security to the delegates from Qing. Then, Jang Hee Jae orders the killing of Sir Shim, but he is saved by the Seol Hee men. Meanwhile, Jang Hee Jae knows that Dong Yi is alive and sends his assassins to kill her. As Dong Yi tries to sneak away again, Jang Hee Jae turns up at her location.

Jang Ok Jeong is worried because the King doesn't trust her anymore. So, she decides to poison herself at her own coronation and blame it on the dethroned Queen. She orders her court ladies to poison her. After that, she becomes seriously ill but she later recovers. Dong Yi meanwhile has return to the capital but the guards are on a lookout for her. Dress as a boy, she manages to sneak into the capital and takes a job as a water maid in order to see the King. She sees the King but as soon as she calls him out, she gets caught and dragged away

In order to make Jang Hee Jae and his accomplices to confess their crime, they are being tortured. But, Jang Ok Jeong still refuses to admit the charges and blames the King for her actions. Then, she orders Oh Tae Seok to kill Dong Yi. So, Southern Faction refuses to accept Dong Yi's evidence because she is a servant and ask her to be handed to them. The King however makes her a special court lady so that everyone will treat her with respect.

The King is in love, but Dong Yi is having trouble in her new role. This is because the court lady doesn't want to work for her. But things get from bad to worse when Dong Yi's maid starts to get sick. The King then takes Dong Yi to their favourite tavern and when they get back to the palace, a strange plague has spread. Strangely, only the court maids are infected. Then, Dong Yi is under suspicion of trying to kill the Crown Prince. Unfortunately for Dong Yi, Jang Ok Jeong is in charge of the investigation and she is only being given three days to find the cause of the plague. She will be killed if she fails.

Jang Hee Jae is summoned to meet Qing delegates who are angry about the fake security records. They warn him that the Crown Prince position can be reversed and if they don't get the book before they leave, the King will be informed. Jang Ok Jeong in the meantime wants to make Dong Yi an official concubine. The real reason is, Jang Ok Jeong wants to know about Dong Yi's past because the candidate's background will have to be thoroughly checked. Then, the King also asks Chief Seo to check Dong Yi's past. He also tells Chief Seo about the cliff and when he heard about it, he is very shocked.

Chief Seo has all the records of the Sword Fraternity. He still blames Dong Yi's father for his father's death. But then, Cheon Soo tells him the truth. Chief Soo then stops Dong Yi from telling the truth and gives the King fake papers about her past. While Jang Hee Jae is trying to find the security records, his sister tries to convince Oh Tae Seok to give the records to the Qing. The plan is not a success. Then, they decide to have a banquet for the Qing delegates so that they can search the palace and Dong Yi's residence for the security records. While she is at the banquet, Dong Yi is suspicious about something.

Dong Yi decides to go back to her residence, but Jang Ok Jeong does not let her. She knows that when all the guards and police are in one place, Jang Ok Jeong accomplices can search for the records freely. They do find the records in Dong Yi's room. However, Dong Yi wants them to find the records so that the police can catch Jang Ok Jeong's brother when he is in the act of handing it over to the Qing delegates. So, when Jang Hee Jae realises that he is surrounded, he tries to burn the records but get caught in the act. He and his accomplices get caught and tortured. Jang Ok Jeong proclaims that she is innocent and supported by the Southern Faction.

Queen Inhyeon returns to the palace and greeted by the King who feels guilty on how she was treated before. Jang Ok Jeong goes back to her old residence and determines to take her revenge. Dong Yi meanwhile is put in charge of the Investigation Bureau. She forgives Lady Yun and her accomplices and as their punishment for helping Jang Ok Jeong, they are demoted to the lower ranks. The King has a dream about having a baby but disappointed when Dong Yi says she is feeling fine. But then, the ceremony to make Dong Yi a level 4 concubine is delayed when the doctor announces that she is pregnant.

One year later, Dong Yi now has a son and the Queen thinks that the Crown Prince should be changed to Dong Yi's son. Then, Dong Yi and the King decide to open a welfare office to help the poor. She goes out in disguise and help to distribute the food. When the head of welfare office is found murdered, the Southern Faction are being blamed. Then, Jang Moo Yeol, who is an Inspector General arrives to investigate the murder. He then visits Jang Ok Jeong to reveal that her father is killed by the Southern Faction and not the Sword Fraternity.

Dong Yi goes out of the palace to investigate the hand signals that being showed to her when she was a child. She and Sir Shim go to the gambling house to ask about it, but no one knows the answer. In the meantime, Cheon Soo goes back to slave village and discovers that Sword Fraternity have regrouped. The new leader of Sword Fraternity is Dong Yi's friend, Gae Doo La. The new Sword Fraternity have been targeting noblemen. But now, they are targeting King's concubine and Gae Doo La doesn't know that she is targeting Dong Yi.

Dong Yi finally tells the truth about her past. But, the King tries to help Dong Yi by seeing Gae Doo La who explains that her father doesn't kill Chief Seo's father. The King then announces that Dong Yi is innocent and knows nothing about the Swordsmen Society. But, she then hands herself to the police because she doesn't want to ruin the King's reputation. The King tries to stop her but to no avail. Chun Soo is also get arrested.

Dong Yi confess to everything. The scholars want the King to punish Dong Yi by execution, but he refuses. Then, Dong Yi's son is dead because he has measles. Soon after, the King decides on the punishment. Cheon Soo is exiled and Dong Yi is sent out of the palace. The King vow to never meet her again. One night, the drunken King arrives at Dong Yi's new home. He then vows to never go back but then hears that she is pregnant. Later, Dong Yi has a son and the King named him Geum. Six years later, Dong Yi and Geum live with the commoners.

Dong Yi and Geum live outside of the palace with the commoners but Geum is desperate to find out who his father is. So, he sneaks into the palace but bumps into Jang Ok Jeong's son, the Crown Prince. Then, Jang Ok Jeong turns up and wants Geum to be beaten because he dares to come near the Crown Prince. But the Crown Prince saves him and he is allowed to leave unharmed. Geum then meets a nobleman and talks to him without realising that the nobleman is his father, the King.

Geum, or now known as Prince Yeoning is shocked when he realises that the nobleman is his father. He starts to get used to the life as a prince and Dong Yi is made a level 2 concubine. Dong Yi wants her son to act stupid when in school. Jang Ok Jeong hears this and asks him to sit in on the prince's exams. But it is backfired when the prince shows his knowledge and this impress the King who wants him to study with the Crown Prince. In the meantime, the Queen who is ill knows about the Crown Prince sickness and informs Dong Yi that she wants her son to study with the Crown Prince so that he can replace the King when the time comes.

But then, it's decided that Prince Yeoning will be studying with a famous scholar and not with the Crown Prince. Furiously, Jang Ok Jeong's mother goes to see a shaman and wants to know the fortune of Dong Yi's son, but she is told that her family will have a bloody end. He then tries to frame Oh Ho Yang for the burning of Dong Yi's house by asking her assassin to hang him with a suicide not. But, the exiled Cheon Soo saves him. Jang Ok Jeong meanwhile knows that her son's condition is no longer a secret and she is ordered by the Queen to tell the King the truth. But the next day, the Queen collapses and Jang Ok Jeong is plotting to get rid of her.

Since the Queen is sick, Jang Ok Jeong thinks that luck is on her side. She then orders a shaman to do some black magic near the Queen's residence because she wants her to die. But Jang Moo Yeol, who is suspicious about Jang Ok Jeong behaviour has discovered the secret about Crown Prince health. Back at the palace, Prince Yeoning finds the doll used by the shaman. But then, the Queen dies. As her last word, she wants the King to protect Prince Yeoning.

The Queen also asks the King to make Dong Yi a Queen, but Southern and Disciples' factions want Jang Ok Jeong to be the Queen. Now, Prince Yeoning and Crown Prince are becoming friends. The Crown Prince wants to know what is his illness is. So, they sneak into the pharmacy and they finally know what his illness is. Meanwhile, Dong Yi goes to see Jang Ok Jeong and wants a truce with her. Then, as the King announces that Dong Yi will be promoted to a Bin level 1 concubine, Jang Ok Jeong tells Dong Yi that she will accept her offer on the truce. But then, Prince Yeoning finds a strange book in his school bag.

Everyone searches for the Crown Prince. He doesn't tell the police who he is because he is worried something bad will happen to him. Cheon Soo finally finds him and brings him back to the palace. He is very weak and ill. Jang Ok Jeong is furious and blames Prince Yeoning. Because of that, Southern and Disciples' faction want Dong Yi and her son to be exiled from the palace because they put Crown Prince's life in danger. When Crown Prince gets healthier, he tells his mother that he knows what his illness is and doesn't feel he is worthy of his position as Crown Prince. He then goes to meet the King and tells him the truth.

When the King knows about Crown Prince's illness, he is furious. Jang Moo Yeol also spread the news so that officials will stop supporting Jang Ok Jeong. So, they all stop supporting her. Furthermore, she is arrested for attempting to kill Dong Yi and the prince. She wanted revenge and ask her brother to start a fire at the palace so that the assassins can sneak in to kill Dong Yi and the prince during the chaos. During the fire, the assassin sneaks in and tries to kill the prince but Dong Yi throws herself in front of her son and gets slash by the sword.

Dong Yi is seriously injured by the attack. The assassin tries to get out of the palace but they get caught by the soldiers. Then, it is revealed that the attack was ordered by Jang Hee Jae. He and Lady Yoo get arrested and tortured but they refuse to say that Jang Ok Jeong was involved in it. But later she is also arrested. The King takes his time to decide what the suitable punishment for Jang Ok Jeong is. The King tries to get Jang Ok Jeong to commit suicide because she is the Crown Prince mother and it is a sensitive issue to sentence her to death but she refuses to do it. Without a choice, the King sentences her, her mother and brother to death.

The Crown Prince is devastated that his mother is going to die and begs the King to change his mind. But the King doesn't change his mind. On the day of her execution, Jang Ok Jeong wants the King to watch her die. The King cries as he watches Jang Ok Jeong drinks the poison. After that, Patriachs' Faction wants Dong Yi to be the Queen and her son to be the Crown Prince but Dong Yi ignores their request. Then, the King makes a new law that forbids concubine from becoming a Queen because of the chaos caused by Jang Ok Jeong. Later, the new Queen arrives and she wants Prince Yeoning to get married.

Dong Yi is shocked to hear that but manages to get the permission to choose her son's bride. She refuses all the candidates from Disciples' Faction family. In the end, she chooses a scholar that has no power in politics. But, the home of the scholar has 'wang gi' royal energy, in which previous Kings have stayed or live there. It also means that the prince will get some support from the public that he should also become a king. In the meantime, Cheon Soo find out that Jang Moo Yeol have been doing some illegal things. Then, the wedding of Prince Yeoning and his bride goes ahead as planned.

The King then announces that Dong Yi is to live outside of the palace. But, the reason for this is, he wants to abdicate and live with Dong Yi. Then, the Crown Prince can become King and Prince Yeoning will replace him as the Crown Prince. But, Jang Moo Yeol discovers the King's plan and he asks the Disciples' Faction leader to help him stop it. Furthermore, He is also desperate to get rid of Dong Yi and her son. So, when the King is away, he prepares a plan to frame Dong Yi. The first step of the plan is, he gets himself put it charge of the army.

Dong Yi leaves the palace and set up her own citizen's advice bureau to help lowborn who have problems with corrupt nobleman. Then, she discovers that the Finance Minister and Police Chief are involved in corruption and they also frame a lowborn for the murder of an official. But, thanks to her investigation, the framed lowborn are released and the corrupt officials are caught. A few years later, the King and Dong Yi are both dead. Dong Yi's son, who becomes the new King of Joseon, visits his mother's grave with Cheon Soo and promises to be a good King.