This sentence has been nagging me since this morning.
She had gone home as she had probably come. Source
Why are had gone and had come used instead of went and came?
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The narrator is speaking about a past reference time when was alone in the house after the woman left. He realized at that reference time that the woman he had seen leave had not gone out into the winter night without adequate clothes but had taken a man's hat and had gone home in the same condition in which, even earlier, she had arrived. All of these events occurred before the past reference time, and consequently are cast in the past perfect.