1) The story that I wrote was published. =I wrote the story and the story was published Here “the story” is the object of “I wrote”. In other words, “I wrote” is an incomplete sentence.
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2)The story that (I had resigned) was published.--> Here, "that" is not the object of the verb "had resigned." In other words, we cannot say, "I had resigned the story." The sentence also can be divided into two: The story was published. I had resigned. (In the