John Alden kills the French commander as the zombified Native Americans are fighting him and Billy. One of the zombies stabs Billy in the back and she is bleeding heavily.
The dark lord is torturing Anne and intends to kill her. Cotton arrives in time to save her by claiming her life (and his child's life) as his reward for returning.
Tituba comes to warn Mary. They believe the Essex Witches are in league with the dark lord and he already knew of her resurrection.
Anne is confused as to why Cotton has returned. He returned to protect their child.
Isaac has hidden away inside the brothel so that he can free the birds carrying the manhoods of Mercy's victims. The birds fly to their male owners and the captives gain their freedom again. They stab Mercy relentlessly in retaliation.
Cotton is forced to write the biography of the dark lord and his failed battle.
Billy is still alive, but she is dying. John Alden removes her jacket to treat her wounds and discovers that Billy is a woman.
The Countess tells Sebastian to bring her some of Mary's blood to help with a spell. He retrieves a bottle of blood from the dark lord's chamber and delivers it to his mother's skeleton.
The dark lord is playing a game of chess against God. Mary arrives to beg mercy from the dark lord and repent. He offers her a deal to become his bride and be a goddess -- no longer just his mother.
Mary and The Sentinel make an uneasy partnership. He reveals that there is a spy in the Essex Hive and she reveals the dark lord's plan. While The Sentinel confronts the dark lord, Tituba returns to the Hive and finds the traitor. The witches perform a spell for the tree to kill the traitor.
Billy reveals the truth about her past to John Alden. She dies from her injuries.
Mr. Putnam is murdered by Thomas Dinley. Thomas did it in exchange for payment from Sebastian.
Cotton wakes up and encounters a vision of his grizzly death on a cross. Mary tries to bestow friendship on him, but Cotton does not trust her.
Mercy offers Hathorne freedom since she is near death. He refuses the antidote as he wants to be with her. Mercy needs blood to regain her health, but she does not have the heart to take any away. The ladies of the brothers offer up their blood freely.
Anne offers her service with herbs to help the refugees. Cotton begins to fall for her again. While tending to the sick, Anne helps a mysterious pregnant woman from Boston. It is Gloriana and she is pregnant with Cotton's child.
Sebastian gives Mary the gift of her past. Mary gets to wear her fabulous dresses again.
Tituba is, in fact, the traitor and the one spying for the dark lord. She has done everything for him and demands her reward. She forces him to perform a blood pact to get what she wants. In exchange, she must kill The Sentinel.