Well we don't know who the stranger is. But the game heavily hints that she is part of a group that is also fighting the darkness. As for who she is talking to, it is the people on the ship she uses. As for what happened to them, we don't really know, my guess would be they are a small team that sort of work in the shadows, which is why they need the Guardians help in the first place. Rasputin is an defensive AI that protects the planet. Most likely the defenses that surround the last city. As far as why the aliens fight each other. Well they aren't friends. The Vex we know despise everyone. And if you look at the other conflicts it is a matter of turf. The Hive and Fallen are fighting on Earth because The hive sent Seeders to Earth from the Moon and started to take over. The Vex are trying to take over Venus, which is why they are fighting the Fallen there, the same thing with Mars, which is why they are also fighting the Cabal. Same with the Fallen and Hive on the Moon. The Fallen are outcasts trying to make their own way, which is why they are on the moon in the first place. The story is there, it just isn't the focus of the game. Which is honestly a good thing. Imagine if cutscenes were more common. Imagine seeing the same scene over and over again as you did missions. The problem is that it is clear that Bungie intends to tell this story of a long period of time, which is why we don't have a lot of answers. This is basically the first chapter.