What the song -- and, I suppose, the video -- is about was explained by John Darnielle at the Mountain Goats website in a post back in July:
This here album track, anyway, is called "Cry for Judas," it is about survival but that's kind of an oversimplification, it's also about building a vehicle from the defeated pieces of the thing you survived and piloting that vehicle through the cosmos, it's kind of complicated but people who know what I'm talking about will kind of intuitively get the idea and the rest of you will I hope be able to get a sense of it through the song.
I think I get it.
The Mountain Goats, "Cry for Judas"
(Lyrics and chords)