Crota's portal allowed some Vex into Oryx's throne world, some of which escaped into reality. Quria laid a trap for Oryx in the Nichta(?) Thought Ship. The bulk arrived in our system during the Traveler's terraforming. The Vex-Hive battles happened a [i]long[/i] time before the Traveler entered our system. Assuming all Golden Ages are a few centuries in length, and the Traveler visited the Eliksni world and Harmony before us... And yes, the Black Heart appeared after Quria. That was an old theory that actually held some backing. The Traveler's doubt and fear solidified into a mass that actually harmed it. Now, however, it seems to be a proto-Darkness manufactured by the Vex. Or even possibly a worm, stolen from the Hive.