Your first time through the game, the story appears to be a post-apocolyptic retelling of a classic fantasy tale. A young Nier becomes a hero as he sets off to rescue his sister from the clutches of the evil Shadowlord and his evil minions.
The Shadowlord is the key to saving humanity. Only he can keep the separated human souls sane so that they can eventually be recombined with their replicant bodies. Without him, all Shades will become mindless monsters and the sterile replicants will eventually die off. When Nier kills the Shadowlord to save his sister, he guarantees the extinction of the human race.
However, the big difference between these two playthroughs is the choice at the end that leads to either the C ending or D ending. With the C ending, Nier kills Kain to free her from her curse, likely going on to live the rest of his days alongside his sister.
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