Supposedly before Destiny's story was in its final stages the speaker was supposed to be evil and attempting to kill the traveler. So the whispers could be something they didn't remove to save time. I just got a stereo headset and there is a lot of sounds in this game that seem strange to me now. I have heard whispers yet though.
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Actually, both the Traveler and the Speaker were evil.
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I've heard a few myself with some decent headphones plugged right into the tv, Earth, tower and moon. But the odd thing is, no one is registered in the open chat thing. :/
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One of the ones that bothers me the most is in the Nexus strike. Right before when your light turns on before the actual boss. There is always a really weird mechanical noise. It isn't too creepy but bothers me a lot cuz it doesn't make any sense.