Rooster Teeth has been experimenting with a much more serious storyline in both the Recovery One mini-series and now this. In fact, Reconstruction seems to be a sequel to Recovery One... the guy who killed all the people in trailer also appears to be the mysterious antagonist from Recovery One.
Warning: slight spoilers below for main series.
Now: "the ship". Many fans seem to think that this is the same ship that crashed in Blood Gulch at the end of Season 4... and apparently exploded in the finale. I happen to think that this isn't a very far-fetched theory... the delayed explosion made me wonder if something with the ship's warp drive (or whatever the RvB series equivalent is) ruined the intended effect of Andy's explosion and deposited the ship in that valley. After all, if a bomb combined with active weather controlling machinery can catapult you 800 years into the future, why not?