The episode begins as the young Mary Walcott and the rest of the townsfolk of Salem gather in the commons as Isaac Walton and his lover Abigail Cooke are placed in the stocks. Isaac is whipped and branded with the letter F for fornication by the head selectmen George Sibley. The town helplessly watches on too afraid of his assailant until the young John Alden steps forward and speaks against the feared Puritan but George warns him that his father's memory can only protect him for so long angering the rash John but he is stopped by Giles Corey from making the situation direr and warns him that George may have tolerated his father but he will not rest till he see's him dead.
Later that evening Mary goes to the graveyard where she is secretly meeting John, she scolds her lover for his reckless behavior who then informs her he is being sent to join the militia to fight the French and Indians. Mary is disheartened with his news but John vows he will return for her within a year splitting a silver coin in half giving one-half to her as a symbol of his vow to her. The couple kiss passionately before they presumably make love.
The following morning a saddened Mary watches on with the other families of the men leaving for the war as her own lover leaves Salem.
Several months later Mary is going to church accompanied by her friend, servant, and slave Tituba. She complains of feeling sick caused by morning sickness but Tituba tells her she will feel better once she is inside. They stumble into George Sibley who tells her she will thank him one day for sending John to war hinting that he knew of their courtship. Tituba proceeds to tell an upset Mary to stay strong as it will be over by tonight.
The same night Tituba and Mary sneak into the woods but Mary begins to have doubts but Tituba warns her that there is no place in Salem for the child she is carrying and that George Sibley had sent John to die in the war and will do worse to her when he discover's she is pregnant with John's baby. Once they are deep in the woods Tituba begins a dark ritual where Mary has visions of dark creatures that both frighten her and attack her terrified of the repercussions of being an unwed pregnant woman she continues to not only give the life of her unborn child to these creatures but sells her soul to Satan thus becoming a witch. A heartbroken Mary weeps when she realises the child she carries exist no more and is comforted by Tituba who promises her the whole world shall be hers in return.
Seven years later
John returns to Salem and is met by a gruesome sight— three poor souls hanging from a tree. As he passes through town he is seen by both Isaac and Cotton Mather. Returning to his home he is confronted by Giles who mistakes him for an intruder as he had believed John had died. The pair celebrates his return with a drink and John questions him on the people he saw hanging upon his arrival. Giles informs him that Salem is under a witch-panic led by Cotton the son of the infamous witch hunter Increase Mather and is shocked to learn that his Mary is now married to the ailing George Sibley.
The same day Isaac is delivering packages to Mary at her home the House of the Seven Gables and tells her that John is not only alive but has returned leaving her shell-shocked.
That evening John is drowning his sorrows in the tavern where he meets Cotton who asks for the aid of three strong men to subdue a girl and is willing to pay for their services. John accompanies him to the home of the Reverend Lewis where he is attacked by Mercy Lewis a girl that Cotton believes is under the influence of witchcraft. John helps him tie the girl down to her bed but mocks the idea believing the girl to be simply mentally ill.
The next day the residents of Salem attend church. Mrs. Hale the wife of Magistrate Hale scolds her daughter the young Anne Hale for dawdling as she wants her in the front row so that she can attract the attention of Cotton a match she seems to want for her daughter but Anne does not seem enthusiastic at the prospect and nearly stumbles into Mary Sibley. Once inside the crowd listen as Cotton warns them of the new dangers that now plague their home— Witches. Magistrate Hale publicly speaks of his fear that the worst thing that could happen to Salem is a witch-hunt which Mary replies on her husband's behalf that there is worst things than a witch-hunt— a witch. John steps forward and once again mocks the idea that witches exist leaving Mary taken aback to see her former lover again but soon regains her composure and sarcastically welcomes the captain back from his long service defending Salem. She later proceeds to invite him to a dinner she is hosting with her husband that John ungraciously accepts.
That evening John goes to the tavern where he meets Isaac but at first, does not recognise him and threatens him after he sits staring at him but soon realises who he is when he shows him the scar on his forehead showing him the letter F that had been branded into his skin seven years ago. Isaac pleads with John not to abandoned the people of Salem again and tries to convince him that witches are real.
The same night Cotton is at the home of Reverend Lewis examining her for the "Witch's nipple," where she has suckled the witches familiars but becomes aroused and goes to The Divining Rod, where he sleeps with the prostitute Gloriana Embry but is stumbled upon by John Alden.
At the dinner party John attracts the attention of Anne much to the dislike of Mary and Anne's father Magistrate Hale who both watch on as the girl flirts with the captain as the dinner proceeds John begins to hallucinate of both Anne and Mary caressing him provocatively under the table an illusion created by Mary, John excuses himself and is soon joined by Mary herself. Mary reveals that she had been led to believe he had been killed and is shocked to learn the reason for John's absence— he had been captured by the Indians for seven years. John tries to convince Mary to leave Salem with him and the couple kisses passionately before Mary pulls away and tells them it is impossible for them to be together before they are interrupted by Magistrate Hale.
Once the party is over an upset Mary confronts Tituba who had been the one that had led her to believe John had died and receives a visit from Giles who informs her that he saw what she and Tituba had done in the woods all those years ago and either she must tell John the truth or he will.
The next day John is leaving Salem and stumbles across Anne who is sketching in the graveyard. The young girl flirts with the captain and which is observed by Mary Sibley herself who is standing nearby. She secretly takes a lock of the young girl's hair with her purpose unknown.
Meanwhile, Mary not wanting John to discover she had aborted their love child devises a plan to use the young Mercy Lewis to accuse Giles of witchcraft to protect her secret.
Mercy who is under the care of Cotton Mather and is forced to wear a metal muzzle, paraded around Salem led by cotton so she can expose the witches, compelled by Mary she points to Giles who is then arrested.
John who is leaving Salem is stopped by Isaac at gunpoint who wants to prove that witches really do exist and leads the captain deep into the woods where the witches meet.
At the same time, Mary enforces her power over Cotton who has imprisoned Giles who refuses to speak to anyone but John and insists that Giles is pressed for an answer before she is led away by Tituba so she can begin the witches sabbat.
Mary returns to her home where she and Tituba begin the witches ritual Sabbat linking her to the other witches in the woods.
Elsewhere John is shocked to witness the witches in the woods but is unable to see who they are as they wear the carcass of dead animals — A stag, a pig, and a wolf but they are discovered forcing John to shoot one of them so they can escape before they are recognised causing the connection between the witches and Mary to be broken.
John and Isaac returned to Salem and find Giles being tortured in the commons for a confession for witchcraft. John tries to save his friend but is unable too and he watches as he dies from being pressed with stones. An angered John announces that he is not leaving, threatening the selectmen while being watched by Mary from her balcony.
Mary returns inside her home and confronts Magistrate Hale where it is revealed he is the witch John shot at. Mary demands to know who had seen them but Magistrate Hale doesn't know and she reveals her plan to use the Puritans to kill each other to complete the grand rite.