Just got around to watching the episode last nite ...
I also caught "the Ship" reference, & wondered how Secret service Guy "seemingly" got to Alaska & back so quickly ... Although when they set Sophia Free it also seemed they got her 'back' to DC too quickly .. So I guess she was already there ..
It was interesting that whoever these 'others' are, they weren't aware of "our" WWII history, or the Manhattan project .. & instead gave us the Bomb earlier that we would have gotten it ...
Also so far there is no trace of their "ship" not even wreckage.. Just fire.
1) From some earth future time, & came/escaped back. (Terminator)
2) From some "Fringe"-like Alternate Universe, with an unknown agenda.
3) Escaped Humans decendants, of people originally plucked from earth 100,000 yrs ago by Aliens (Stargate).
4) The Flintstones descendants. (The Jetsons)