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Atticus's treatment of Mayella reveals that though a victim of many cruelties, she has chosen to bring cruelty upon Tom, and must not be excused for this. As he points out, Mayella wants to protect herself by placing her guilt on Tom, knowing that her actions will bring about his death because the jury will believe her, a white woman, and not him, a black man. Thus, she manipulates the unfairness of her society toward her own ends.
In the end, Mayella's biggest conflict is within herself. She's afraid of her father, and we want to sympathize with her situation. None-the-less, she chooses to do what's right for Mayella, even if it means an innocent man will go to jail.