John Proctor thinks the entire court proceedings are flawed to the point of being unethical. In Act 2, Marry Warren returns to the Proctor household to inform them of the "weighty work" they are doing in court. Proctor scoffs at this and tells Mary not to go back to the court. She says she must go back. He replies, "What work you do! It’s strange work for a Christian girl to hang old women!"
Mary seems convinced that the devil is at work in Salem. Proctor, frustrated, threatens to whip the devil out of her. Mary is going along with Abby's story because she doesn't want the other girls (Abby included) to turn on her. But in Act 3, when Mary and John are back in court, she takes John's side and admits that the girls were lying. She says to Danforth and Hathorne that it was all "pretense" (pretending/lies). As Mary predicted, Abby turns on her and pretends that Mary is sending her spirit upon her. Mercy Lewis and Susanna Walcott join in and claim Mary is spiritually affecting them as well. Proctor knows they are pretending and shouts it out, but they continue. Eventually, Mary can't take it anymore and turns on John. She embraces Abby and promises not to hurt her again. Mary is naive and easily manipulated. This is why she continually changes her story.
John Proctor is furious when he finds out from his wife, Elizabeth, that Mary Warren has been gone all day due to her involvement in the court proceedings. First of all, he is angry because he knows the girls are frauds and what kind of harm they are inflicting on innocent people. Secondly, he is upset by the fact that he pays Mary Warren to work within his home, yet she is spending day after day sitting in the court proceedings. He is also angry because he ordered Mary Warren to stay away from the happenings in Salem and she did not listen.
Mary Warren has changed a good bit from Act I and Act II of the play. In Act I, readers would consider her subservient. She was the girl that wanted to obey. She was the girl that wanted to admit what they were doing in the forest the night before. She was scared, worried and obedient to the adults. However, when readers find her again in Act III, she is strong-willed and disobedient. She claims to John Proctor that she is single and old enough to make her own decisions without being told what to do. Mary stands up to Proctor and refuses to change her mind when it comes to helping with the court.