So the Story is not at all comparable to the story Bungie had in mind before all of the stuff happened to their company. A good way to start integrating that story would be to consider the existing story as a prologue to the missions you can add periodically to eventually restore the story that would explain factions, traveler, the exo, rasputin, and much more. These missions that you can add maybe every 2 weeks and you can focus on making them like Halo story missions. These missions could be accessed in the tower or a separate thing the vanguard strikes in orbit. These missions involve more entertaining things like jumping into a giant crater(sound familiar?), base jumping from a mountain, exploding a ship, or maybe even flying a ship(you have done this before with a different game). It could be a good way to feature some exploration in the last city or the reef. You could eventually reveal those other factions that you were going to add. I think this would be a good way to keep the existing story and the expansion story from the two dlc packs and still have a strong central story with the periodic missions. Halo 4 did something similar with the weekly missions they added, but you would take this concept to a whole new level and make destiny that would be considered to be strong in multiple aspects.