Burning in the Skies

I can see this two ways. Firstly is directly following Oppenheimer's quotation in the last song, it could be in reference to the atomic bomb, specifically those dropped on Nagasaki and Hiroshima. "Blood of innocents burning in the skies," "swimming in the smoke" all being views a crewmember of the bombers could have had.

Possibly more likely/fitting is an environmental view, whereupon the blood of innocents burning in the skies, swimming in the smoke, rising of the sea, literally coming from the destruction of forests and burning of fossil fuels (though still being poetic, mind you.) Also, "I'm losing what I don't deserve" could be in reference to how humans don't deserve our environment with the way we've treated it, and as such it's disappearing. And "But in the end we were meant to be apart" could be in reference to how humans have almost always tried their best to distance themselves from nature, or at least the idea that the two cannot coexist.
With either, it's quite the sad song, much more emotional than any love song.

Speaking of which, @ellzZzZ, I'm doubting that there's any intentional love imagery/lyrics in this song, or even album. In A Thousand Suns, they went for a view of the world as it is. Not to mention that Linkin Park hasn't had that much love imagery in any of their previous songs either, and when there is any it's very rough and extreme, not the kind of "aw I love you" that comes with most other music.