Alright here it goes... Crota is either The Darkness or a high-ranking enforcer of some sort to The Darkness. While Crota may create the hive, the hive don't just come from thin air... they are created from Fallen and Cabal that have been corrupted and consumed by The Darkness, here their likenesses as well as the cooperation by the Fallen and Cabal. But what about the Vex? The Vex don't just come from the future, they come from a parallel timeline in the future where Humanity has already by consumed by darkness... because they are humanity consumed by darkness! OH -BLAM-! (We know the Vex are at least partly organic) They come back before the split in the timeline not to destroy us, but to thrust us into darkness. Why? Because why would The Darkness settle for just one reality? So now you have the Fallen and Cabal fighting the Hive and Vex because Darkness. And they want to destroy us because somehow they've figured out that we may become Vex.