"Everything that belongs to us will be ours, but only if we create the capacity to receive it."
Looking back at all the Destiny information we have made me think of what the story would be about. One key thing I noticed is man had a "Golden Age" that at some time ended and we were reduced to 1 city on Earth.
I notice these phrases like: "Together we will take back all that we have lost." and I can't help but think we were once the invaders in this universe. We were the people taking over distant worlds then our advances got pushed back. Maybe that is why they keep coming after the last city, out of hatred for mankind's expansion. The text suggests that the humans (maybe a faction) feels entitled to the distant worlds from our golden age of mankind. Maybe these worlds belong(ed) to other races of aliens before us, maybe they got reclaimed.
This is all a hunch mind you but what if we are the villain?
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That does sound like a pretty good/cool idea. Although it wouldn't be very much fun to fight as a villain. I could something more along the lines of "we extended our power to far and unleashed an evil we could have never known, that is kicking our asses" to stick with the manifest destiny analogy - the native americans we were trying to remove on our push twards the west - turns out they have semi-automatic rifles and they are pissed enough to try and squash us like we tried to squash them. .... That just makes American History sound more depressing.