If a story can make me cry or become emotional through its already won in my book. Nier did it so hard though, It kept breaking you down constantly hitting you with these sad revelations. The story was epic. But sad as well.
From the Queen in the Desert being killed by wolves, to Emil/No.7 sacrificing himself to save Nier and Kaine. To Kaine having to deal with her physical differences to normal people, the ridicule she went through because of it and the anger that was bred into her.
It might have been developed by Cavia with SE staff members assisting and published by SE. but it was litterally the best story SE has released in a game since probably ROTZ.