A MURDEROUS SECRET — A face from John's past comes to Salem, and Mary's plans nearly come apart when she loses control of Mercy Lewis. Elsewhere, Mary's most trusted ally, Tituba, is forced to deceive John in order to eliminate a threat that endangers her mistress.
The episode begins with Reverend Lewis as he performs a Catholic exorcism on his daughter Mercy Lewis. Holding a cross and a bible he chants in Latin while Mercy pleads with her father to stop in fear of what the Puritan's will do to him if they discover what he has done but her father tells her he is not afraid of the Puritan's and is adamant he will free her from the witches' grasp. He asks if she trust him and she tells him yes before he pulls out a knife, his intention unknown. A frightened Mercy begs her father to stop but he continues to cut her belly until the witches snake familiar slithers out from within her and fleeing the room leaving Mercy finally free from Mary's control.
The next morning a stranger on horseback arrives in Salem and heads to the docks where a ship has taken passage. The ship has a package onboard that he has been tasked with acquiring but he is told by a militiaman that the ship is under quarantine due to an influenza outbreak under the orders of Mary Sibley.
Meanwhile, Mary taunts her husband on her next choice of victim; his friend the blacksmith as she watches John Alden as he passes through town heading to Salem's graveyard. Where he stumbles into Anne Hale while paying his respects to his parents. John enquires after her health as he had been informed she had taken ill but she reassures him that she is well despite the sudden illness that had come over her. She explains her fear all may not have been as it had seemed despite her father's reassurance intriguing the captain but they are interrupted by Magistrate Hale who insists on escorting his daughter home.
Later John approaches Cotton Mather at the Tavern on the subject of miss Hale being under a witches spell as he believes that might of been the cause of her mysterious illness but Cotton seems to be skeptical of the idea and even more so of John's suspicion that her father is a witch but his attentions are diverted when he sees Gloriana Embry in the arms of another man and quickly loses his temper causing him to attack her admirer but he is stopped by John who pulls the reverend away before the stranger excuses himself and leaves.
While at the market Mary is with Tituba where they stumble into Mercy and her father who is taking his daughter for a walk. Mary once again tries to use the girl to accuse another of witchcraft but her attempt fails and the rest of the residents of Salem watch helplessly as the girl collapses in the street with her father by her side. Following the revelation that Mercy Lewis is no longer under the control of Mary, the witches meet in the woods. Magistrate Hale speaks of the witches doubt of her plans for the grand rite. While Mary insists that the girl can still be used. The Magistrate continues to warn Mary that if he cannot abate John Alden's suspicions of him he will have to do something about him and is advised by Rose to earn his trust.
Back in Salem Mary pays a visit to Cotton. She reprimands him for not taking care of his charge after the episode in the market who insists that there is no evidence that it was the cause of the witches. She reminds him to do what he was brought to Salem to do to; find and punish the witches of Salem.
Elsewhere the Magistrate meets the captain in the tavern and informs him a reception in John's honor has been arranged to celebrate him joining the selectmen board. The captain does not seem enthusiastic about the idea but soon leaves when he notices the man he had previously stopped Cotton from attacking earlier that day. Following the man outside, he corners him where it is revealed that the captain knows the man as William Hooke. John demands that he leave Salem but Hooke tries to threaten him into arranging a meeting between himself and Mary so he can obtain a package onboard the ship under quarantine unless he wants him to reveal his past to the residents of Salem but the captain warns him too stay away from her and too quickly finish his business in Salem and leave.
That night Mary is on her way to the reception and stumbles into William Hooke who tries to coerce her into allowing him access to the ship but she is insistent that no one should access the ship with the influenza epidemic. While Cotton pays a visit to Mercy Lewis and pleads with her to reveal who torments her but the girl sleeps soundlessly. He notices the aroma of agrimony a herb commonly used with exorcism and questions her father who insists that the apothecary had advised it and after inspecting Mercy he discovers the wound on her belly.
Meanwhile, at the reception, Mary greets Anne Hale who has convinced her father to allow her to attend the party. Mary admires a necklace that she is wearing and Anne explains it was a gift from her father. The necklace burns Mary's fingers when she touches it but it goes unnoticed. She approaches the magistrate and is shocked he would use Valerian root, a tool used by the witch hunters. She watches jealously as Anne flirtatiously greets the captain when he arrives but is pulled to one-side by Cotton who informs her that Mercy has been expelled of the witches familiar by the means of a catholic exorcism and is reprimanded by Mary for allowing such a thing to happen as the thing more worst than a witch is a catholic and John continue to shock the selectmen board when he publicly addresses those present at the party with his belief that those accountable for being witches may be the ones that have been charged with leading the people of Salem. While Gloriana visits Cotton at church following his reprimand from Mary and questions his reaction to seeing her with another man who then shockingly rapes her on the stairs and afterward throws down coins of silver as she lies their tearful from his attack.
Back at The House of the Seven Gables William Hooke breaks in hoping to speak with George Sibley and upon arriving finds him holding a piece of cloth with the word WITCH written upon it in his own blood after he had stolen a knitting needle from Mary who returns home to discover what has transpired and given the choice by Hooke; give him access to the ship or he will tell those of importance what she is. Left with little choice she agrees with what he wants but tasks Tituba to remove the problem permanently while she tries to acquire control of Mercy once again.
After returning home from the reception John is shocked when Tituba pays him a visit. She tells him she had previously witnessed his confrontation with Hooke and that he is blackmailing her mistress to gain access to the ship, threatening to spread lies of an affair between her and the captain and pleads with him to put a stop to their shared adversary. While Mary once again forces the young Mercy Lewis under her control by forcing another familiar within her, despite the girl's pleas.
That night following John's visit from Tituba Hooke obtains the parcel that he had been tasked with acquiring and is stumbled upon by the captain. Hooke reveals that the captain had committed murder and treason but had spared his life under one condition— that he never laid eyes on him again. The captain continues to straggle the man to death and disposes his body among the victims of the influenza outbreak before he takes the package a strange and mysterious box. While at the Magistrates home he confronts his daughter over her obvious attraction to the captain and forbade's her from having any more contact with him as he believes he will only bring her heartache as he is still in love with Mary Sibley.
After his murderous act, John is returning home and is seen by Mary the former lovers speak of the vow they had once made to each other seven years ago and the captain enquirers if they had been lies but she reassures him they had been wishes made by those who had no knowledge of the world. He wishes her sweet dreams before she returns inside where she is confronted by the apparition of Mercy Lewis who tells her she knows what she is.