I actually finished the game a couple of weeks ago, and I think I've had time to think about the ending.
The ending perfectly fits the theme and tone of the game. It was a great way to end it because it managed to hit that morally grey area and spark interesting debates without being too controversial (ME3's endings). It deals with many topics and values and it really takes time to think about it.
From a story point of view, I never saw Joel as the villain. I think Joel made the right choice for the wrong reasons concerning Ellie. I am not sure about this, but it seems that it was 99% sure that Ellie was the key to the cure. Obviously, like many of you pointed out, Joel saved Ellie because of the fact it was his daughter figure, to give himself a reason to exist, etc. However, something I'd like to point out is how a cure can horribly backfire. Assuming Ellie provides a cure, then what? The fireflies, being the sole distributor, might just decide to horde the cure for themselves or sell it at a high price. We see how little they care concerning Ellie as a person, only as a means to an end. Who's to say they won't treat humanity the same?
Furthermore, I know everyone says ''Of course humanity should live'', but think about it. The world of the Last of Us is not the same. How exactly would you distribute a cure? Most humans have been infected. Some have turned to killing their own for survival. Few would actually be eligible to begin treatment. We all see how complex this is in our modern society with lesser outbreaks. I wouldn't bet much on it actually working. If humanity is destined to survive, it will. It all depends if they can adapt and survive in their environment, like they always have.
Finally, who says humanity deserves a cure? We've seen the world of the Last of Us. It's a cruel and despicable place. Humanity has turned in on itself and collapsed. We've been destroying our planet and causing harm to everything and everyone around us. Our society demands that the strong crush the weak, that people suffer to make others thrive. Even in the Last of Us, this is obvious. Remember the quarantine zone at the beginning of the game? Rations constantly being cut without explanation, people dying on the streets without a care in the world. Thieves and hunters would kill you just for a bullet or two. The infection simply made us worse as a species. Is this a species, a world, etc. that's actually worth saving?
Well, that's all my mind can handle, for now. Love this game
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