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The second playthrought of NieR.

*Spoilers*

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Killing Beepy and Kalil. In your first playthrough, you are led to believe that the older brother was killed by a robot (Beepy), and this robot is controlled by a shade (Kalil). The younger brother asks you to kill this robot and the shade, so you do because shades are the bad guys.

However, extra cutscenes are played on the second run. You find out that Kalil's mom sacrificed herself to save Kalil. Kalil is left alone crying until Beepy comes in and asks what's wrong. They become friends, and you see their relationship building up. Then it is revealed that the cause of the older brother's death was due to the ruckus the brothers were making. Beepy and Kalil had a conversation, saying that it was unfortunate the brother died, and that they weren't going to hurt the brothers. Basically, the shade and robot were nice guys, and not the terrible monsters you were led to believe throughout the whole game. It was a little sad seeing them die together after that.

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*End Spoilers*