As far as Elena and Chloe, I think it was pretty clear Nate had some feelings for Elena. I don't think it was abrupt. Sully mentioned it in UC1, Drake asks Chloe if she thinks Elena and CAMERAMAN JEFF are a couple when they met up with them in UC2. There's some prior history with Chloe that they don't bother going into, and they never touch on what happened with Elena in between the games. You could have replaced Chloe with any other character close to Drake and he would have gone to the same lengths that he did to rescue her, though. He's just that kind of character.
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Knowledge is the eye of desire and can become the pilot of the soul.