At the end of Act 2 after Elizabeth Proctor has been arrested and taken to jail, John has finally realized Abigail's true intentions and knows that he can no longer keep secret the fact that Abigail is faking and that he had a relationship with her. His wife's life is at stake, and though he is a proud man, John will not let her die because of him.
John tells Mary Warren that she will go before the court and tell them that she and the other girls are faking. Mary is Proctor's servant; so during this time period, the Proctors had almost parental authority over her. While Mary knows that what she and the other girls is wrong, she is frightened for her life. She, like Elizabeth Proctor, knows the evil that Abigail is capable of and realizes that Abigail has the power to turn the other girls and the court against her if she challenges them. Plus, Mary Warren also knows (from Abigail) that John Proctor committed adultery with her and that in Salem's Puritan system that is a grievous offense.
Despite these pleas and excuses on Mary's part, Proctor is determined to save Elizabeth and the lives of his friends; so he first threatens her and then commands:
"Make your peace with it! Now Heaven and Hell grapple on our backs, and all our old pretense is ripped away--make your peace!"
His words demonstrate that he does not care about his or Mary's fate because they both have brought this upon themselves, but they must do all that they can now to save the innocent accused.