Those moments did indeed look dire, but mostly for Drake. Could this game be about losing everyone around him because of his inability to forego his wanderlust obsession?
If I had it my way, I would make it pan out like this:
1) Introduce one or two more characters to be developed who are close to Nate (perhaps a relative or friend), in addition to Chloe, Elena, and Sully.
2) Nate's irresponsibleness gets some of them killed, tortured, etc.
3) He deals with the repercussions throughout the entire game
4) By the end he has to seemingly sacrifice himself for Sully, Elena, or someone, and is finally thought to be dead
5) And as I said in my earlier post, I would have the end scene pan out like that, with Sully in a museum wandering around and feeling uneasy when the alarms start going off as he then realizes Drake is still alive (but for some reason hiding? lol pirates after his ass!)
I shouldn't have gotten too specific, but that's how I would like to see it end.