Mary is a young, unwed girl pregnant with John Alden's baby in Salem, a Puritanicaltown. Believing her lover John was killed during King William's War, she is now faced with the Puritans' stocks and forehead branding, or giving her and John's child to the devil. Having chosen the latter, she marries the town's richest and most influential selectman George Sibley, claiming his wealth and power for herself by enslaving him. Reverend Cotton Mather is trying to stop witches from taking over America by killing them. John returns home to witness a witch-hunt, wherein Mary plans to use the trials to get Puritans to kill each other, allowing her to rule Salem.
Following the first death of the Grand Rite, Mary intends to sacrifice another innocent before the next full hunters moon in the form of a sign. Meanwhile, John works with Cotton Mather and Issac Walton in order to locate and stop the witches.
When Magistrate Hale discovers that it was Isaac who broke the witches circle, it's up to John to save him. A power struggle arises within the hive, forcing Mary to assert her authority with potentially deadly consequences.
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.
Following the discovery of The Malum, John acquires the help of Cotton to find out more about the Grand Rite. Mary tries to regain control of Mercy, and Tituba is tasked by the hive to finally discover the secret of John Alden that he has killed to keep.
After successfully capturing Rose, John and Cotton plan to extract information on the Grand Rite from her during the planetary alignment with Saturn. Mary assists Mercy in becoming a witch, and initiates her into the hive.
Mary rediscovers her passion for John, and her new apprentice Mercy could help accelerate the Grand Rite. Magistrate Hale tries to delay an possible threat to the hive. His daughter, Anne, becomes more suspicious of those around her.
Upon his arrival, feared witch hunter Increase Mather wastes no time taking control of the witch hunt and Salem. Mary fears that Increase will discover her husband has been spelled, and enlists the help of Isaac to deter him from uncovering the truth.
Mary must act quickly in order to prevent Increase from undoing the spell placed on her husband. Mercy and her followers prove themselves useful to the greater cause, and Cotton mourns over the banishment of Gloriana.
While Mary deals with Mercy's betrayal, Tituba must endure the torture inflicted upon her by Increase in his newly founded "House of Pain". Meanwhile, Anne stumbles upon one of her fathers artifacts and suddenly finds herself far from home.
With the help of Issac, Mary devises a plan that she hopes will rid her of both Mercy and Increase. John has been falsely accused of witchcraft and awaits trial, while Anne learns a dark truth about her heritage from her father.
The trial of John Alden is held, with Increase as his prosecutor and Cotton as his defense. However, the ordeal brings a few unexpected secrets to light, and Mary is ultimately faced with a difficult decision.
Mary must choose between fleeing Salem with John or completing the Grand Rite, and Tituba reveals a long kept secret that could sway her decision. Meanwhile, Increase closes in on the witches, and the Hales prepare to go into hiding.