In the wake of the Grand Rite - merely the first phase of the Hive's dark undertaking - a horrendous plague sweeps through Salem. Tensions escalate between Tituba and Mary, who tries to enjoy what limited time she is allowed to spend with her young, recently returned son. Mary confronts Mercy Lewis in a bid to strike a bargain with the upstart Witch, but Mercy already has diabolical plans of her own in play. As Anne Hale begins to comprehend the nature of her own true power, she is extended an offer that may provide her some clarity and relief. Meanwhile , as Mary attempts to exert her mortal influence over the citizenry of Salem, she makes the acquaintance of an intriguing true man of science, Dr. Samuel Wainwright, who may threaten her cause. Back in Boston, a haunted Cotton Mather must answer for his failure in Salem; and Mary learns John Alden's fate... . or so she thinks.

In the wake of Mercy's brutal act of violence, Mary works to rally the citizenry of Salem against her rebellious, wayward former protégé, and to put an end to the willful Witch's uprising. Despite the unwanted distraction, Mary moves forward in her bid to complete her Hive's dark task with the promise that her eventual success will result in a permanent reunion with her son. As Dr. Wainwright looks for clues to cure the growing plague, his methods create concern for the Selectmen. While his only hope seems to be the discovery of the pox-ravaged Isaac, who, beyond all expectations, clings to life, the possibility of his success creates additional concern for Mary and Tituba. Meanwhile, John Alden prepares for an epic confrontation still to come, and has a telling encounter with an unexpected ally; Mary's son begins to show another, unsettling side of his nature; and Anne Hale - ripe with her new and as-of-yet uncontrollable powers - embarks on an unforeseen journey... but discovers more than she bargained for.

As the town of Salem continues to try and cope with the mounting plague, suspicions and fear grip the townspeople, and one of Mary's recent adversaries takes steps to place himself in a position of power among the citizenry, leading Mary to rally her allies and resort to making a risky play in her bid to maintain control of the town. Meanwhile, Anne and Cotton find they share some common ground, an earlier act of mercy may come back to haunt Mary, tensions of a less-than-Puritan nature continue to smolder between Mary and Dr. Wainwright, John arrives back in Salem and makes his first move in the epic task that lies before him, and Mary and Tituba make a troubling discovery.

In the wake of the most recent attack against her, Mary seeks answers to who may be responsible. To that end - and despite Tituba's warnings - Mary begins to tutor Anne Hale in the ways of witchcraft, but her work may not culminate exactly as planned. Upon his return to Salem, Cotton meets Dr. Wainwright and despite their obvious initial differences of opinions, each discovers the other may have something to offer in their mutual task. John Alden continues to make his presence felt in Salem, and his actions have repercussions for him, and for others, in ways both political and physical. Mercy moves forward in her plans of revenge against Mary even as one of her acolytes has second thoughts about the part she's playing in the Witch's plan. Meanwhile, Mary and Wainwright continue to explore their mutual interests, and Mary and Tituba search for a hugger.

Following Mary's public chastening, the recently-minted Magistrate Hathorne steps up his bid to wrest power over the citizenry of Salem from her, forcing Mary to once again compel her bewitched husband to take action. When Hathorne levels a not-so-veiled threat against Anne Hale - which he mitigates with an unappealing solution - it prompts the young Witch to seek Mary's council. She receives sound advice... but it comes at a fearful and unappealing cost. Mercy Lewis' grisly preparations to enact her revenge reach new heights, drawing two reluctant participants closer in the process, and forcing the hand of one of her increasingly tenuous allies. Meanwhile, as John Alden continues to pursue his righteous task, his search for answers yields valuable results, and Mary takes the fight directly to her newest foes... with surprising results.

After Countess Marburg shows up in Salem, she threatens Mary's stronghold that she has on the city.

Mary resorts to drastic measures in a bid to attain valuable information for use in combating the Countess, and she tries to shore up her political hold over Salem with a move that could either assure her success or seal her fate. As Anne Hale continues her Witch's tutorial, she learns that getting what she desires comes at a cost, and that in order to continue on her seemingly powerful path she must still remain supplicant to others. As the Countess and her son, Sebastian, continue to work their plan, they are presented with a rare glimpse into their enemy's stronghold where a fascinating introduction is made, and their cause is made stronger by a new but unpredictable ally. Wainwright returns to Salem having gained some measure of information that may shed light on the town's particular strain of plague, but further investigation reveals shocking results. Meanwhile, Tituba makes plans for her recently captured prey, and Cotton gets a surprising visit.

When a plan of Mary's threatens to backfire on her, she strikes a tenuous deal in order to achieve her greater goal. While she learns a bit of the history which surrounds her newest and most dangerous foe, the key to defeating the Countess still remains hidden. Both Anne and Cotton receive unexpected late-night visitors, each of which results in very different conclusions. As Mary tries to bond with her son, she and Tituba discover that the seemingly scared and vulnerable little boy is harboring unsettling thoughts and predilections... and perhaps even darker secrets. Meanwhile, with the help of her familiar, Anne Hale begins to discover some of her father's hidden - and unsettling - secrets; Tituba tries to strike a deal with the captured John Alden; Dr. Wainwright discovers that, perhaps, science alone does not hold all the answers he seeks; and Mary makes a much-needed - and unexpected - ally.

As the "Starry Messenger" comet approaches Earth, heralding the culmination of the Witches' dark plan, the Countess Marburg makes a long awaited acquaintance with one who plays a pivotal role in her and the others' cause. Mary and Wainwright grow closer, their mutual affection heightened by recently discovered revelations, but as the pair plans for the next steps along the journey she has in store for him, another - displeased with these recent developments - takes matters into his own hands. Even as Mary prepares to strike against the Countess, she receives news that shakes her to the core. As Cotton tries to reason out information recently revealed to him, the betrayal of a recently made ally may spell his mortal doom. Meanwhile, Anne continues to glean knowledge from her dead father's writings, and a long-brewing feud reaches a tipping point, culminating in a surprising and potentially game-changing disclosure.

As the Countess Marburg prepares for the imminent arrival of the 'Starry Messenger' and her lover, Mary stages a last ditch effort to thwart the eternal Witch's plans. Anne Hale faces making a time-sensitive decision that could have far reaching consequences. Cotton Mather faces his imminent demise.

As the Countess and her son move against two of John Alden's valued allies, Mary suffers under the yoke of Puritan oppression stemming from an alliance between the Marburgs and another of Mary's powerful enemies in Salem. But even as she seems to be at her most hopeless, Mary tries to take advantage of a widening schism between mother and son. As John and Cotton proceed with their monumental and unfamiliar task, each must process new information and gather strength to aid them in what lies ahead. Meanwhile, wracked with guilt and sorrow, a mournful Isaac pays a surprise visit to an already somber town gathering, Anne Hale finds the fate of many may rest in her novice - but powerful - Witch's hands, and John and Cotton get the first glimpses of the enemy they are facing.

With the Starry Messenger comet drawing ever closer, John Alden fights for his very life, while Anne Hale works to comfort and protect one whose life or passing brings with it great consequences for Witch and mortal alike. She soon learns another unfathomable secret about her past, and finds she's faced with a terrifying decision that could greatly impact the Countess's plans. Mary, palpably affected by recent events, finds herself in a wholly unfamiliar situation, leading her to try a risky gambit. Meanwhile, when John shares shocking and unbelievable information with Cotton, it leads the younger Mather to seek out answers on his own, but he discovers only more questions; Mercy pursues desires of her own, but finds another's prediction to be fatefully and disappointingly accurate; and Isaac finds himself in a wholly unfamiliar position among his fellows.

With her mission seemingly accomplished, the Countess Marburg revels in the apparent completion of her plans, unaware that the object of her devotion has desires which may be in direct conflict to hers. And one of her most trusted allies grows increasingly weary of the Countess's treatment, leading to an unexpected act of defiance. Emotionally drained by recent events, an all-but-defeated Mary stages a last-ditch effort against the Countess. Meanwhile, John is visited by a pair of unexpected allies who deliver a fateful message; Mercy comes to learn a stark reality, leaving her to face an uncertain future; an unrepentant and increasingly powerful Anne faces the personal consequences of her duplicitous actions, leading her down an even darker path; and when Cotton learns an unwelcome truth, his reaction is initially mixed, until a startling confession strengthens his resolve... but it may already be too late.