Increase Mather is on a ship, and all of the passengers are dying. He knows a witch is on board and will kill everyone on board in order to catch him.
Mary is having a heart-to-heart with Hale. She's angry to learn about the Malum being brought to Salem without her knowledge, especially since it was she who came up with the plan to use the Puritans against each other to achieve the Grand Rite. Hale bows before her and accepts her supremacy.
Mary threatens Hale's life if anyone should go behind her back, or that of his wife and sweet daughter.
Hale's wife tells Anne that her father is a spy. Anne calls him a traitor and receives a smack in the face.
A message from the ship arrives carved on the back of a whore. He's trying to stop Increase, and chooses to keep the knowledge of his impending arrival from Mary because he believes she has enough power at the moment.
Tituba does a spell on Mary so she can get close to Alden and learn where the Malum is. She goes to her past, when they made love. She scratches Alden's chest in the dream and they both awaken.
Back on the ship, Increase deduces that the captain is the witch.
Mercy's friends are over and she's using spells on them. Mary decides to teach Mercy how to walk wherever she will, without her body.
Mary's plan is to use one of the girls to accuse a family of witchcraft, the Barkers.
Cotton is speaking to God when Alden happens in.
Alden suggests if doubt is all Cotton he has, he should use that as his weapon.
Alden asks Cotton what he knows about dreams. Cotton thinks they are the undiscovered country. Most men dismiss them but if a man lives 70 years he'll spend at least 20 of them in another realm, their own private America.
Mary goes to Alden again in his dream, asking for the Malum. They are making love on the grave of Giles Corey and Mary realizes Alden has hidden it there.
Overcome with desire, Alden kisses Anne before heading to the whorehouse to take care of business.
Mary sends Mercy to Mrs. Trasks' to control her. She slits open her throat, which is more than the spell called for, leaving her unable to accuse Mrs. Barker.
Mary is unable to stop her dreams and going to Alden's side. She's shocked when Anne enters her dream and she loses Alden. As Mary in her dream is chased by Indians, she gets lost in the dream, frothing from the mouth as Tituba tries to reclaim her.
Mary left Mercy alone on her walk all because she wanted to see Alden one more time.
Alden goes to Mary and she greets him with a passionate kiss, jumping upon him and they start to make love.
While retrieving the Malum from the grave, Tituba realizes what Mercy did when she hears the cries of the citizens.
Isaac goes to Cotton with the hope of bringing control. Cotton cannot get them to think with reason. They just want the Barkers killed. Hale tells Cotton it's best to leave a crowd once they start rioting, but Cotton cannot. He demands they be held in the jail overnight so they can justly face the accusations in the morning.
Glorianna thinks that Cotton was very brave and he tells her he cannot be her customer any longer. He needs time to sort things out, and when he does everything will be different. Just then, Increase steps into town.
Mary wants to stop what she's doing with Alden. He thinks all that matters is him and her and they should live for each other. She wishes it were possible, but it isn't. She cries and tells him to leave. She has gotten all she needs from him. He wants to know what she's not telling him because it makes no sense.
Increase steps into his son's home. He ordered the Barkers burned. If they are innocent, then God will see to their recompense. Increase thinks Cotton has turned into an imbecile with all of his reason. Letting a single witch walk free is not acceptable.
Mary stands in the window as Alden reaches what remains of the burning Barkers.
Increase is in Mary's bedroom. The King of England has granted them a new charter and a new governor will arrive in the spring to help them eradicate the heathens and savages for now and forever.
Mary learns from Increase that witches hindered his return to America. Increase believes George is the luckiest man in Salem for having Mary, and wants to see his old friend.