I think the story is pretty straightforward:
1. Earth was visited my a giant alien robot ball called the Traveler, which was friendly, diplomatic and shared a bunch of alien tech with us.
2. We used that tech to seriously level up everything over the next couple hundred years, increase our lifespan 3x over, colonize Venus, Mars, Mercury and the Moon, feed everyone, etc.
3. Turns out some crazy cult/god/misty space power entity called the Darkness exists too, and its purpose is that it HATES the Traveler and wants to kill it. And it lost track of the Traveler for a couple hundred years while it was here being nice to us, but once the Darkness figured it out, it came here, and fucked everybody up; party over.
4. Now the Earth is damn near extinct, there's only one city left and in it. The Traveler got almost completely destroyed; it's still in orbit, but it's all smashed open, can't talk and can't do anything. Although in the one particularly nasty battle where it really got demolished and put into that state, it sent out a bunch of little robot drones called Ghosts that can go around and sift through all the corpses on Earth and resurrect one each... hopefully one with some military value that can fight the Darkness aliens (even though things ain't looking so hot).
5. All those fighters the Ghosts resurrected are called Guardians, and they live in a big tower in Last City, while everyone else (civilians, families, etc) live downstairs in the city proper.
6. Hey, YOU'RE the newest guardian that one of the Ghosts resurrected. He'll hang out with you like Navi, but you can call him Dinklage-Bot if you prefer. Good luck, sucker!