On Salem Season 2 Episode 8, Cotton and Dr. Wainwright go to search for the source of the plague. They head into the woods and discover a pit which looks like it could be a portal to hell. The men are convinced this is what the witches have in store for the people in Salem, but they agree to keep this information between the two of them because they don't want to start a riot.
Unfortunately, Dr. Wainwright takes it upon himself to go to Mary and tell her he knows the truth about her, but instead of wanting to expose her for her crimes, he wants to join her. He gives Mary a ton of compliments and tells her that she is a true scientist and this makes Mary trust him and they sleep together. Later, Mary gets a visit from Increase who finally tells her where she can find Countess Marburg's soul, it's the ship, but he disappears before he can divulge any other information.
After Sebastian walks in on Mary and Dr. Wainwright having sex, he decides to take part in kidnapping John and bringing him to the countess. He manages to get John out of the house and convinces him to go with him.