As the Countess Marburg prepares for the imminent arrival of the “Starry Messenger” and her lover, the Dark Lord, Mary stages a last-ditch effort to thwart the eternal Witch’s plans, but her success or failure may rest in the hands of others who each have something important at stake. After getting devastating news, Anne Hale finds she is faced with making a time-sensitive decision that could have far-reaching consequences, and it takes knowing words from another interested party to strengthen her resolve. Even so, the young Witch finds herself at a crossroads and faced with yet another important choice to make – a choice that may determine the fate of all in Salem. Meanwhile, Cotton Mather faces his imminent demise - the result of Magistrate Hawthorne’s jealous treachery - until an unlikely party intervenes. But his rescue could come at a price that he may be unwilling – or even unable - to pay.
Countess Marburg is on her ship bathing the young John explaining what will happen to him during his baptism, telling him that he will be reborn with her by his side but the boy tells her he doesn't want her he wants his mother. She then holds him under the water before she allows him to resurface and kisses him passionately causing his eyes to turn an eerily black.
Elsewhere Cotton is dragged from the carriage on his way back to Boston by two of Salem's guardsman and held at gun point. Realizing that Hathorne has ordered his murder, he begins to pray and waits for his death but a hooded figure appears and kills his assailant's and reveals himself to be John Alden. Cotton is bewildered at how John found him but he retorts that he is no longer the same man as he was before for better or worse. Cotton continues to ask him what he wants from him and the captain explains that he needs him to perform an exorcism on a boy which will stop everything that the witches have planned. Cotton asks why he hasn't just killed the boy as he once told him he killed a man just because he knew his name but John asks him if saving someone has ever given him hope and he agrees to do as he wishes but he has something to do first.
Back in Salem Mary secretly meets with John and he informs her that he has got Cotton on board with the plan. He enquires if she is sure that the boy is their son but Mary insists that he is and he will see the moment he looks into his eyes. She gives him back his tools of powers and tells him the ones that gave him them knew what they were doing and reveals to him that she will perform a trick she witnessed the countess doing so she can find her Achilles Heel without revealing her intentions to the countess while he is in the crag protecting their son but warns him that the Marburg's are not like the other witches he has killed. She asks him for his forgiveness but knows she will not get it but John sadly tells her that they have both done things to each other that they cannot forget and she replies that if she survives the night she will find him and their son.
As the citizens of Salem gather Hathorne announces to the crowd that both the good doctor Wainwright and their Reverend Lewis are gone and that the Sibley's have led them to ruin while the countess and her son converse in the front row quietly. The Countess question's where Mary is and chastised's him as he was meant to keep an eye on her when the Magistrate emplores them to stand and pray. Mary arrives reciting the common pray along with them taking the seat next to the countess. Mary plays along with her ruse that she will sacrifice her son to complete the grand rite but the Countess warns her that she is not forgiving like the Puritan's God and will delight in killing her. Outside Sebastian gloats on the fate of Wainwright to Mary who appears to be saddened by the loss of her lover and ally. She questions his motives as he is loyal to his mother and he had promised her he would help her son if she gave him Wainwright but he has broken his promise to her and he assures her she will be reunited with her son in time.
At the Hale cottage, Anne receives another unwanted visit from Hathorne who tells her that Cotton has been killed by Indians while returning to Boston. Clearly upset by the news he asks her to marry him stating it would be what Cotton would want. When Cotton arrives announcing that Hathorne tried to have him murdered the pair confront each other but Hathorne denies it and quickly leaves. Anne embraces Cotton who reveals that he must do something that he may not survive and plead's with Anne to marry him today beforehand. While Hathorne secretly visits upon the countess and her son aboard their ship.
Anne meet's Cotton alone and the pair say their vows in the woods privately- Anne pleads with Cotton to come back to her and he tells her he will try. Afterward, Anne returns home to find Mary there, she tells Anne that she is different and Anne informs her that she is married now but she fears Cotton is performing a dangerous task. Mary reveals that he is and that she knows she stole her father's book of shadows but Anne continues to inform her that she had no choice because of the countess but she didn't give it to her. Still terrified from her encounter with the devil the previous night Mary tells her she knows he came to her because she sensed it and it is the price a witch pays for the power he gives them and is comforted by the older woman. She warns her she cannot trust the countess and that they are currently at war but Anne is adamant that she will fight neither for her nor the Countess but Mary warns her soon she will not have the choice if she wants to save her husband as the Countess has already said she will kill him.
That night Mary spies as the Countess escorts her son to the crag and sneaks onto the ship while projecting herself at their meeting place. Once inside she is stumbled upon by one of the countess men but uses her powers to set him ablaze and finds numerous of the countess soon-to-be victim's but takes pity on them and frees them and is alerted to the presence of Isaac. Clearly upset at the treatment of her friend she quickly frees him who reveals to her that Mercy Lewis is alive and in cahoots with the countess and lures all her victims to the ship. Mary tries to persuade him to leave but having realized what Mary does not truly trust her and refuses to leave until he finds Dollie.
Back in the woods, the Countess along with her son continue to follow Mary's specter while Mary searches the ship. She cast a spell that shows her a secret passage and makes a blood offering to pass through but it leads her to a fairy glade and there finds the sarcophagus where her original body is hidden but when she opens it revealing the carcass she tries to touch the relic but her flesh begins to burn and disintegrate as it is magically protected. Gathering her courage she carries the carcass back to the ship despite the pain and her plan is successful. Back onboard the ship the magic disappears and Mary takes the carcass to the woods where her specter is while a distraught Isaac finds the body of Dollie among the bodies of the countess victims and weeps for his lost love in his arms.
In the wood's the Countess realizes that she has been following Mary's Specter and congratulates her on surprising her and Mary demands that she release her son or she will destroy her relic. As the pair confront each other she proves she is willing to destroy them both if necessary and pulls out one of the teeth from the carcass mouth causing one of the countess own tooth to fall out while Sebastian appears behind her holding a knife to her throat. When Mary conjures fire in her hands threatening to burn her relic a fearful countess demands that her son step a side telling Mary once she puts her relic on the ground she will release her son. Suddenly they hear the sound of hooves and John appears on horseback who kicks Sebastian away from Mary while she quickly sets the carcass ablaze and screams at John to go and get their son to safety before she is captured by Sebastian again, the countess rushes to save her relic as John rides off with his son.
John takes his son to Petrus's hut and ushers him inside. The boy asks who he is and John reveals he is his father, the boy runs to his father and an emotional John embraces his son with tears in his eyes. While back in Salem, Sebastian has escorted Mary home, alone in the Sibley house Sebastian tells her that John will fail and they still have two more nights to complete the grand rite before the comet passes over Salem. Mary mocks him announcing he cannot have both her and his mother but he tells her that he believes in having your cake and eating it. When Hathorne arrives and arrested her for adultery revealing that Sebastian is a witness to her affair with Samuel Wainwright she has dragged away as Anne watches from a far. Afterward, Hathorne visits the Countess and offers himself to her showing they have become allies to thwart Mary. While Cotton meets John at the hut and tries to persuade him from doing an exorcism on the boy but when the boy wakes up and turns his head 360 degrees revealing eerily black eyes and in a demonic voice announces they are too late and he will soon feast on their entails a horrified John and Cotton watch on.