Looking into the concept art for destiny I think you can find a lot of clues about the ultimate story of destiny.
Firstly during the GDC event they showed concept art of the original theming/design of the enemies. The concept art showed 5 enemy races. The fifth depicted as humanoid people all in black, with pyramid ships, and black smoke like the smoke we see when we enter a darkness zone in game.
My theory is that this race is actually 'dark' humans opposing us the 'light' humans.
I think this can also explain both the fallen, cabal and possibly the hive and vex. Maybe theirs a dark side to every life form in the universe but the dark side of all those races prevailed over the light in those races and that is why they fight against us.
I can see this theory being more so for the fallen and cabal but less so for the vex and hive. Maybe the vex were created by the dark humans just as we created the warminds?
As for the hive, perhaps they were the first victims of the darkness and have now become so dark they they cannot be saved?
Thoughts?
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Have you ever thought about what the deal with Xûr is? He's a Jovian, in all black, and humanoid, that's got to be what the 5th race would be, it fits in so perfectly