On Salem Season 2 Episode 9, Mary and Dr. Wainwright discuss what needs to be done before he can give himself over to the dark side. She informs him he'll need to destroy all his researched into the plague and she will take care of Cotton. 

At Cotton's house, the Magistrate visits and Cotton convinces him that the witches are planning on a war and brings him to Dr. Wainwright to back up his story. Unfortunately, Cotton isn't aware of Dr. Wainwright's new ally and the doctor denies knowing what Cotton is talking about. They end up going to the pit Cotton was talking about, but none of the blackness is there and only the decaying bodies remain. Cotton is immediately taken out of Salem and the Magistrate plans to kill him by making it look like an accident.

Meanwhile, Sebastian convinces Mary he will help save her son if she lets him do away with Dr. Wainwright and Mary agrees. Sebastian takes him to the pit and sends his body to hell. 

Mary confronts Tituba about what Countess Marburg has planned for John and Mary gets angry about how she was lied to. Tituba admits she knew everything, but it was Mary's decision to give her child to the dark lord. Before Mary can kill Tituba, Tituba reveals that John is still alive and brings her to him. Mary cuts him down and tells him about their son. Mary convinces him she didn't know the child was alive, but he is currently in trouble and they need to go save him. John pushes away his instincts and decides to go search for his son.