To My Beloved Thief, Episode 3, unfolds with Prince Yi-yeol finally locating Eun-jo at the Hyeminseo. Her initial fear, assuming he had discovered her true identity as Gil-dong, is swiftly replaced by relief when she realizes he is unaware of her secret. As she guides him into the clinic to attend to his wounds, she brings up the encounter at the clinic the previous night. He hopes for some emotional clarity, but is angered when Eun-jo labels their kiss as an impulsive mistake and apologizes.
As she tends to his arm, Eun-jo mentions that the Hyeminseo is lacking in medical herbs due to the sheer number of patients they have. On her way home, she runs into Dong-ju, who is thrilled about the food the police aide sent to her house.
Meanwhile, Secretary Im orders that all remonstrances be sent to him for review before submission to His Majesty. Chief Censor Kim attempts to protest this request, but Secretary Im shows him a book listing all his crimes and blackmails him into submission.
Elsewhere, Dae-II picks a fight with his father, Min-jik, for returning all of Eun-jo's dowry. The family is still facing financial troubles, and he failed the exams. According to him, the dowry would have helped the family. Min-jik clarifies that accepting the dowry would be disrespectful to Eun-jo, who already works hard to support them.
At Secretary Im's house, Jae-I, who got first place during the examinations, learns from his brother Seung-jae that Eun-jo is betrothed to marry their grandfather. Seung-jae vows to make Eun-jo's life a living hell once she is married. He wants to use her to get revenge on Min-jik for upholding his honor and returning the dowry.
To Eun-jo's surprise, herbs arrive at Hyeminseo courtesy of Prince Do-wol. Later, after the Queen Dowager refuses to accept his greeting, Prince Yi-yeol decides to inspect the delivery of herbs at Hyeminseo. Dae-chu suggests that he come clean about his royal identity, thinking that news of his charity might help ease the Queen Dowager's anger towards him.
On the way to the clinic, Prince Yi-yeol helps Hae-rim hide from her brother, Jin-won. Sadly, Prince Yi-yeol does not remember their earlier encounter. This makes Hae-rim wonder why she is not memorable.
At the clinic, Prince Yi-yeol aids Eun-jo in calming a patient experiencing a seizure. He then accompanies her while taking stock of the herbs that have been sent. As he finds himself concerned about the opinions others hold of him, as they shape their perceptions of him, he endeavors to dispel the nasty rumors that have been circulating. Just then, Jin Won enters the scene, reminding him of the lady he was seen riding with earlier. With a cold demeanor, he reprimands Prince Yi-yeol for publicly displaying his affections for the young lady. Eun-jo tries to speak up for him, but Jin-won prohibits Prince Yi-yeol from entering Hyeminseo.
Meanwhile, Eun-jo comes into possession of a ledger that lists Chief Inspector Kim's crimes. The chief inspector had attempted to burn the proof, but Dong-ju saved it. Initially dismissing it as worthless, she planned to use it as toilet paper. She jestingly shows Eun-jo the book and, given that Eun-jo can read, she quickly realizes its significance and secures it for herself.
Later that night, she disguises herself as Gil-dong and hands the ledger to Prince Yi-yeol. Upon reading it, he claims that he has no intention of doing anything about it. However, after reading the accompanying letter from Gil-dong, he changes his mind. He meets with the king and hands him the ledger.
The king wonders why Prince Yi-yeol is taking an interest in court politics. Prince Yi-yeol claims that he is only trying to get back at a lowlife who humiliated him. The king decides to defend his brother's pride and punishes Chief Inspector Kim by returning his land and all the property he acquired to the people and by exiling him. Eun-jo reads out the punishment to the commoners, and they are all overjoyed that the chief inspector has finally received his retribution.
The exile of Chief Inspector Kim creates panic in the parliament. Secretary Im instructs Seung-jae to keep an eye on Prince Yi-yeol and take note of whomever he meets. He wants to figure out how the ledger found its way into the prince's possession.
Similarly, Prince Yi-yeol directs Yoon-bok to track Gil-dong's movements to verify whether he got the ledger by chance or if someone is backing him. In the meantime, the commoners arrange a celebration and invite Prince Yi-yeol, but it's Dae-chu who attends in his place. Eun-jo unexpectedly learns from Jae-I that Min-jik returned the dowry. Jae-I warns her to call off the wedding, since what awaits her in their house is misery. She rushes to confront Min-jik, but her mother stops her.
Later, Prince Yi-yeol goes searching for her at Hyeminseo. He finds her seated on the rooftop, lost in thought about her dreadful future. She does not reveal her troubles, but he makes her feel lighter when he offers to help. She ends up joking about having a powerful backer. On the other hand, Prince Yi-yeol finds himself more fascinated by her and decides to confess his feelings. He asks if she's seeing someone and makes his intentions to pursue her clear.
Before she can respond, Jae-I opens the door and sees them together. He assumes that Prince Yi-yeol is Eun-jo's lover and threatens to expose the truth of her betrothal to his grandfather. The episode ends with Prince Yi-yeol demanding to know who Jae-I is. Jae-I pulls Eun-jo closer, daring Prince Yi-yeol to guess their connection.
