I'm going to touch on a few things leading up to the end of the game, the final scene itself, and Joel's decision to save Ellie. These are just my thoughts and theories about how the story played out and what I took away from it.
Warning! Don't read any further if you want to avoid spoilers, granted you shouldn't even be here unless you've finished the game already.
Breaking Down Ellie's Changed Demeanor
So come spring time we notice Ellie just isn't the same, she lags behind a bit, isn't paying attention to anything Joel is saying, and at times appears to be lost in thought. What's happened? Well, quite frankly she's been through a lot and their journey has taken a toll on her, the things they've seen and the things they've had to do to endure.
Their winter was rough. Joel nearly died, and the whole experience with the creepy cannibal guy that captured Ellie has had an effect on her. Up until then they've managed to luck out and scrape by, but the winter experience brought her back down to Earth, she no longer sees them as infallible or indestructible. She realizes their goal of finding the Fireflies could come crashing down at any moment. It's why her conversation with Joel about her dream with the plane crash is so important, it represents her uncertainty and lack of confidence about ever making it.
