In The Crucible, why is Mary Warren so afraid to go to court when John Proctor tells her to accompany him?

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You need to remember what stage the Salem witch trials have reached at this time - more and more people are being denounced as having been seen with the Devil and are being brought to trial by the group of girls, of which Marry Warren is one. Hysteria and fear are sweeping through Salem, and the group of girls has incredible and frightening power - the power to denounce you, leaving you in the position of either facing death or "confessing" your supposed crimes of being in league with Satan. Also, Elizabeth has just been told that Abigail has charged her with witchcraft. John Proctor thus decides to sort out this "madness" and go with Mary Warren to tell the court that this was all made up. Note how she responds:

I cannot charge murder on Abigail.

When pressurised by John Proctor, she goes on to say:

She'll kill me for sayin' that! Abby'll charge lechery on you, Mr. Proctor!

Mary Warren identifies that it is Abigail who is leading the group of girls and is directing their wrath of denunciation. For her to go against the group by herself would be very dangerous, as we go on to see in Act III, when the girls turn on her, exactly as Mary predicted.