John has promised to come to the courts and "bring [Elizabeth] home." He feels incredibly guilty that she was arrested in the first place; he blames himself because it was Abby's affections for him-spawned from their affair-that led to his wife's accusation and arrest. He realizes with full force just how far Abby will go, and that his wife was right: "[Abby] wants me dead, John." So, he has a very personal sense of vengeance, and justice fueling his desire to get his wife cleared of any charges. And, it just so happens that Mary Warren, who has been with Abby from the beginning, knows just how fake all of the accusations of witchcraft are. Mary was there in the forest, she knows why they started crying people out (so that they wouldn't get in trouble for the dancing), and John needs her to testify to this in court. If he can somehow prove that Abby is being false, it will nullify Abby's accusation against Elizabeth, and Elizabeth will be set free.
However, when John goes to Mary and insists that she testify against Abigail and the other girls, Mary is terrified and refuses, insisting, "They'll turn on me...I cannot do it!" What she means by this is that she is afraid that if she goes in to the courts and states that they were all faking it all along, the girls will start pretending that Mary Warren is a witch, and unite against her, and she will end up being on the stand, in jail, and hanged for witchcraft. She knows what power Abby and the girls hold, so she is terrified that she will be their next victim, especially if she testifies against them. And, she is right. Act three will reveal just how right she is.