I don't really understand why you think it odd that he wanted to stop El Dorado from getting off the island. He follows right down the path of Francis Drake - he set out for something, something big, but realized afterward how horrifying it is. His intention is just not to let Roman and Navarro take it and sell to some terrorists. Nate's character always falls on the good side of things. He's seemingly after gold and riches, but when push comes to shove, he'll make the good moral choice. At the end of the day, that's why people like him - and it's one reason people always seeing a conflict between the story and the gameplay, though ND's defense of that had usually been 'Drake doesn't shoot first.'
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Knowledge is the eye of desire and can become the pilot of the soul.