Jang Ok Jeong confirms to Dong Yi that she is not going to accept her truce as they are enemies. Then, guards storm the Crown Prince's palace because someone has stolen the Crown Prince books. But, the Crown Prince saves the prince by telling the King that he has give it to him. Jang Moo Yeol goes to see Dong Yi and to convince her to reveal the truth about the Crown Prince, but she rejects it. The Crown Prince and Prince Yeoning meanwhile sneak out of the palace to go to a festival. But the Crown Prince get arrested and dragged away to a police station. The palace is in chaos when they find out that the Crown Prince is missing but he is about to be punished for stealing.

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.

Jang Moo Yeol is now in charge of the army and he also has the Queen under his influence. He then persuades the Queen to move Dong Yi to her new residence while the King is away. Jang Moo Yeol's plan is to frame Dong Yi for the murder of the Crown Prince. The Crown Prince entourage are attacked but he is not harmed. Cheon Soo and his men, who are at the scene are arrested. Since the King is away, the Queen is in charge and she issues an emergency decree to get all of those who have involved in the conspiracy arrested. The guards surround Dong Yi's residence and but they are there not to arrest Dong Yi. They are there to arrest Jang Moo Yeol instead. This is because the Queen has discoverd what Jang Moo Yeol's plan is.

Then, Dong Yi decides to tell the Queen about the King's plan to abdicate. She also manages to send word to the King about Jang Moo Yeol's plan to frame her and Prince Yeoning. Then, the King's army decide to follow Jang Moo Yeol's men and catch them trying to pay off merchants who involved in the Crown Prince assassination attempt. As his punishment for treason, Jang Moo Yeol is beheaded and his accomplices are exiled and executed. The King cancels his plan to abdicate because everyone is against it. Then, the Queen decides to adopt Prince Yeoning so that he will be a legitimate heir to the throne. In the meantime, Dong Yi decides to leave the palace.

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.

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.

Dong Yi, Sir Shim and Chief Seo now realises that Oh Tae Seok and Jang Ok Jeong is behind the Namin official murder, framing of Sword Fraternity and the death of her father. When Oh Tae Seok knows about it, he is supposed to be taken to a safe house with Jang Moo Yeol's men but they kill him. Gae Doo La and his men who are following them are shocked when they see him killed. They end up fighting Jang Moo Yeol's men and are now being blamed for Oh Tae Seok's murder. When Jang Moo Yeol looks at the Swordsmen Society records, he notices that the leader has a daughter named Dong Yi. Then, Dong Yi sneaks out to help injured Gae Doo La to escape. But then, the King and his men turn up on only to see Dong Yi is helping a traitor.

Dong Yi is tied up and about to be killed by Jang Hee Jae. But Sir Shim saves her by saying that he has the security records. He tells him to release Dong Yi and he will reveal where the records are. Dong Yi is released and Shi Shim reveal where the records are. Then, he is locked up in a barn as Jang Hee Jae men search for the records. After that, Jang Hee Jae men come back to kill Sir Shim, but Dong Yi has already helped him to escape. Chief Seo and Cheon Soo finally arrive in town. But, Dong Yi is on her way to the capital with Seol Hee. Before they left, it is revealed that the records that Jang Hee Jae has found are fake. He gives Dong Yi the original records and to be taken back to the capital.

Sword Fraternity assassins nearly kill Dong Yi but then stop when she says that she is the daughter of the original Sword Fraternity leader. Dong Yi later meets Gae Doo La who refuses to stop what he's been doing. Jang Moo Yeol meanwhile informs the King that the exiled Namin leaders have given their wealth to the poor in order to atone for their mistakes. They are all invited back by the King. Jang Moo Yeol then realises that something is not right because Sword Fraternity assassins kill the guards but not Dong Yi. In the meantime, Dong Yi who has been working hard to investigate the hand signal finally gets her breakthrough. She realises that the signal uses music notes and it spells out Oh Tae Seok's name.

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.

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

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.

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.

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.

Dong Yi runs to the home of Chief Seo's colleague with the proof that Jang Ok Jeong and Jang Hee Jae are behind the bribe. But, the assassins arrive and kill everyone. Dong Yi manages to run away but a dart is shot into her shoulder. Because she is very injured, she staggers across the mountains in order to reach the King who is on his way back to the palace. But, because she is too weak, she collapses and lies motionless in the grass. Then, the King discovers that Dong Yi and Chief Seo secretly investigates Jang Ok Jeong role in the Queen's dethronement and also the poisoning of his mother. Furthermore, he is also worried about the disappearances of Dong Yi.

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 finds out that it is her mother who causes the plague. She however ignores it because of her hate towards Dong Yi. In the meantime, Southern Faction finds no early records about Dong Yi and Cheon Soo. So, they try to get the information from Dong Yi's friends. Dong Yi meanwhile discovers that the plague is caused by the poison in the cosmetics that are linked to Jang Ok Jeong's mother. But, she is arrested because her three days limit is over. The King has been informed about the investigation and when he goes to question Jang Ok Jeong, she says that she and her mother know nothing about it. Then, delegates from Qing are coming to acknowledge the Crown Prince.

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.