After ten years of service fighting in the French and Indian War, John Alden returns to his home in Salem, intent on reuniting with his love, Mary. On his arrival, he's stunned to discover that the town has been swept up in a wave of witch hunt hysteria, and that Mary has married the town’s richest and most powerful resident.

With witch fears rising, Alden seeks the truth of what’s really going on in Salem while Cotton continues to wrestle with his guilt and Mary looks to execute a plan. The witches get closer to finding out who interrupted the ceremony, but Mary continues to find her emotions for Alden affecting her focus. A clue in the woods leads Cotton and Isaac to find more evidence that the witches may indeed be real.

Salem trembles in the aftermath of the trial, and Anne turns to John Alden for comfort. Mysterious circumstances lead Alden to suspect Magistrate Hale is not who or what he appears to be. Mary discovers who witnessed the witches’ ceremony and deliberates a course of action. George Sibley begins hatching a plan to escape Mary’s clutches.

An old nemesis of Alden's arrives in Salem with secrets that could destroy him. Mary loses her grip on Mercy.

The members of Salem's coven of witches meets in the woods and decide to eliminate one of their most dangerous threats. Alden and Cotton realize the true, dangerous nature of the mysterious object they uncovered – and use it to ensnare something of much graver importance. Mary realizes that her own coven has been plotting without her.

Alden and Cotton find themselves face-to-face with a real witch. An unlikely ally keeps the coven from tracking down their missing sister. Tituba feels left out when Mary decides to initiate a new member into the coven. Alden and Cotton learn that the trials have actually been helping the witches – and soon find themselves under attack after they lose control of their captive.

When a shakeup within the coven leaves Mary with more power than ever, she hatches her most nefarious plan yet to bring the witches closer to achieving the Grand Rite. Alden and Cotton, reeling from the aftermath of their interrogation, question the efficacy of the trials. Alden finds himself weaker by the day, as a victim of Mary's dream spell. Anne makes an eerie discovery about her father’s activities. When Increase Mather makes an unanticipated entrance, Salem and its coven faces the arrival of the most feared witch hunter.

Increase Mather makes it his first order of business to catch a real witch, and starts by pinpointing a prominent figure from Salem’s most sinful district. Accusations within Salem intensify. Cotton must deal with a painful turn of events. Anne’s suspicions of her father reach fever pitch.

Salem sees a second death since Increase's arrival in town. Mary struggles to get George back under her control. Mercy and her acolytes flex their growing power. Increase grows closer to Isaac, putting Isaac’s loyalty to Mary in question.

Increase gets closer to understanding who really runs Salem. Anne finds herself in danger, and Mr. and Mrs. Hale realize that Alden may be the only one who can save her.

Increase continues on his warpath as Alden finds himself the target of fresh accusations. Cotton finds himself frozen in a tug of war between his father and his loyalty to Alden. Anne learns the truth about her father.

Alden’s trial begins, triggering a chain of events that breaks nearly every remaining allegiance left in Salem. While Mary arms the Malum for the Grand Rite, the coven elders urge her to use Alden as the final sacrifice. Increase seizes Mercy’s acolytes for information to use against Alden.

Alden learns Mary's biggest secret, and Mary discovers a new one of her own.