I'm uncertain on the nature of the conflict between the "Darknesses", but there has been some speculation by the characters in Destiny itself:
"Everything is becoming more ruthless and in the end only the most ruthless will remain (LOOK UP AT THE SKY) and they will hunt the territories of the night and extinguish the first glint of competition before it can even understand what it faces or why it has transgressed. This is the shape of victory: to rule the universe so absolutely that nothing will ever exist except by your consent. This is the queen at the end of time, whose sovereignty is eternal because no other sovereign can defeat it. And there is no reason for it, no more than there was reason for the victory of the atom. It is simply the winning play." - Toland the Shattered, Ghost Fragment: Darkness 3 Grimoire card
It's one of those things that's so fundamental, so atomic, the answer will likely never come.
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