Even before Elizabeth Proctor's arrest in Act Two, John has her fetch Mary Warren so that Mary can tell Ezekiel Cheever, the man who has come to arrest Elizabeth, that she had just made and given the poppet to Elizabeth that very evening.  When told about what happened to Abigail—that she had a needle pushed into her stomach and she said that Elizabeth's spirit did it—he exclaims, "Why, she done it herself!"  John asks Mary to confirm for everyone present that she stuck the needle into the doll herself, which she does, and she claims that they can go to Abigail for proof of her story because Abigail sat next to Mary as she sewed the doll in court that day.  At this, John orders Mr. Hale to tell Cheever, "Bid him begone.  Your mind is surely settled now.  Bid him out, Mr. Hale."  Even before John goes to court with Mary Warren two weeks later, he tries to discredit Abigail by pitting Mary's story against Abigail's just prior to the arrest of his wife.

After John's wife is arrested, he knows that he has to act to save her. He brings in Mary Warren to tell the truth about Abby and the other girls. Mary quickly loses her confidence when Abby turns against her. In an effort to show what kind of girl Abby is and that she had motive to accuse Elizabeth, John confesses to lechery and sacrifices his good name. He says that he has "known" her. The magistrates bring out Elizabeth to back up John's accusation, but it backfires when Elizabeth lies. John had said that Elizabeth cannot tell a lie and he was confident that Elizabeth would tell the truth no matter what. She lies thinking that she's saving John's reputation.

Proctor, in his anger and desperation, grabs Abby and calls her a whore. He then confesses his sins to the court and admits to his affair with Abby and tells the court that his wife Elizabeth had set Abby out for being a harlot.