I am surprised no one else has heard them, but there has been at least two times when I have heard someone whisper a word to me in the game. I don't remember where (maybe Venus?) or what the first one said but I do remember the second one. At the tower, I stopped talking to the Shipwright and was leaping over the twisted cords to the left and heard someone whisper "escape."
Now the first one I heard I was playing with a friend online and he did not hear it. However, the second one my brother was watching me play and heard "escape" too. So maybe only I could hear it on my screen?
I don't know if this has anything to do with it but I am a level 26 Hunter and have both the expansion and have completed the main storyline.
Has anyone else heard this?
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The whispers are confirmed to come off the new raid guns. For example, if I am using the raid fusion rifle in the area you're at, you'll hear whispers, however I won't. But hearing it in the tower... Unless Husk of the Pit/Eidolon Ally gives of whispers... I just have no clue