Gonna spoilertag all of this just in case:
There are 4 endings to Nier. After beating the game once, you are giving the option of a New Game+ starting from around the halfway point, where the plot branches off and you get ending B. Playing through again and getting 100% of the weapons opens up endings C and D, D being the one to delete your savefiles. I believe the game does warn you about ending D beforehand. Of course, if you back up your saves on a memory stick beforehand, you can simply transfer them back over after seeing ending D. Also there's an achievement/trophy for getting ending D iirc. It's kind of like Drakengard in how it handles New Game+ with story branching instead of just making you start over. Also, for those of you who want to play as the other Nier (the one in the Japan-only Nier Replicant) the DLC recently released for Nier, Recycled Vessel, allows you to use him for one stage.
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