As scout is drifting off to sleep, two images come to her mind
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"I was very tired, and was drifting into sleep when the memory of Atticus calmly folding his newspaper and pushing back his hat became Atticus standing in the middle of an empty waiting street, pushing up his glasses. The full meaning of the night's events hit me and I began crying."
I believe these images made her cry because in both situations Atticus was giving in and doing things he simply didn't want to do. It's tough to realize your parents find it necessary to give in occasionally, especially when you fight against giving in yourself.