On my first playthrough of the story mode I finished with one mission score of B and two mission scores of A (the rest were S) while my treatment of Emilia was...mixed, and I finished with the "good" ending. On my second playthrough I scored S on all the missions and treated Emilia poorly and received the "normal" ending. So it seems that your dialogue choices with Emilia affect your ending more than anything else, imo.
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