Yay! Really glad someone else on these boards is playing this. Once you finish it, you'll have to tell me what you thought of the whole story.

I've found it really interesting hearing different people's takes on Ellie. I found her extremely likeable throughout the game, and felt like Naughty Dog was trying really hard to make the things she did endearing. If they were, it worked on me. Maybe that is why that one thing she did that I found really distasteful stood out so much to me. However, I've heard others mention how unlikable they find her, or as you said, some found her to be a jerk in general.

As far as raiding houses and the nature of possession in the post outbreak world, yeah, things have kind of degraded to a cut throat take what you need survival mentality.
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At one point Joel casually admits to having done some pretty awful things in those 20 years since the outbreak began. I thought the game did a great job of completely mudding the waters of what right and wrong is in some ways.