Well, with The Last of Us 2 being accidentally confirmed, it seems only fitting that some analysis be given to the original. There's a lot to analyze about Naughty Dog's post-apocalyptic shooter, but in this case, we're gonna look at what makes the ending of the game so damn powerful. But first, let's talk about the game itself. Needless to say, spoilers galore. Stop reading now if you haven't played or beaten the game yet.
The Last of Us ruined the post-apocalypse genre for me. Not just in games, but in all forms of media. I don't care how good The Walking Dead is. I don't care how fun Left 4 Dead is. The Last of Us did everything you could possibly do with a post-apocalyptic setting, and did it right. The biggest thing it did right: showing an unadulterated sense of humanity.
I've described this game to my friends as one of the most human games ever made. It's completely fantasy free. The infection is based on a real fungus. There are no big action setpieces. It's free of contrived Hollywood elements... mostly, and every line of dialogue feels real.
What makes the game 'human', though, is its characters. They aren't part of roaming bands of freedom fighters or bandits or post-government oppressors. This ain't Fallout. They're just people, trying to do whatever they can to survive. We see all sides of what an apocalypse can do to a human.
We see those who shut out emotions and personal feelings to avoid being hurt.
We see those who adapt. 
We see those who try to hang on to a sense of normality. We see those who scrape for any sign of hope. 
We see those who were worn down by despair and violence and became something horrible. 
Most of all, though, we see Joel. We see how he was hurt, how he copes with the decaying world around him, and how he becomes so desperate to have an anchor, to stay sane, that he does the most selfish, selfless thing anyone could do in his situation.
Throughout The Last of Us, Joel's only constant companion is Ellie. Thanks to some smart programming and perfect writing, Ellie oozes charm and depth, and quickly becomes an emotional crutch to both Joel and the player. It can be easy to forget that the endgame is to deliver her to the Fireflies. For the long journey, you might forget that there was even a destination at all, until you reach the hospital.
The Fireflies take Ellie away from Joel, with the intent of extracting a cure from her brain. Unfortunately, that means she'll die, and Joel will be left alone. In the twenty years that he's survived the infected world, Ellie is only thing he loved, and now she has to die. Joel is... not well. Yeah, he's stable, he's collected, he can hold his own in a fight, he's a survivor. That's why he's scary: give him something to fight for, and he'll get it. Until now, all he had to fight for was his own life. Now that he's fighting for someone else, he kills fully armed soldiers to get to her. Worse, if you allow it, he kills doctors. How many doctors do you think are left in this mad world?
As he escapes, Marlene tries to reason with him, saying that killing Ellie to get the cure for the infection would be the best possible ending for her. Given what Ellie witnessed and experienced during the journey, Marlene's arguments have credence.
But here's what we don't know: What do the Fireflies intend to do with the cure? They openly hate the government. They're distrusted by just as many people as those that worship them. Who's to say they wouldn't keep the cure for themselves? And that's assuming a cure can even be made to begin with. We don't know. That's the key. Joel kills Marlene anyway, so we won't ever find out.
So, where's the morality on this? Who was doing the right thing? That answer becomes even more ambiguous when Joel outright lies to Ellie about what happened. And we don't know if she fully believes him. Still, what was he supposed to say? "You remind me of my dead daughter and I love you, so I doomed humanity just so I could be happy" ? That would push Joel straight into villain territory. But he's not a villain. He's just a man trying to survive, and Ellie is his survival.
The beauty of The Last of Us is given form in these last moments because how much we don't know. We don't know what's going to happen next, who is the moral victor, and how this is going to affect Joel and Ellie's relationship. All we do know is that humanity is fucked, and it's either one man's fault, or nobody's fault.
Games usually have a goal. Whether it be to reach a high score, beat a series of levels, defeat certain foes, complete missions, and so on. Your mission in The Last of Us was initially to deliver Ellie to the Firefly hideout. But it wasn't long before you might have forgotten that. Soon, your goal was simply to protect her, because so long as she and you were together, you were happy.
Now, let's assume that a cure could've been made from Ellie's brain .When you, in control of Joel, took her away from the Fireflies and destroyed humanity's last hope, you fulfilled your self-assigned mission. You protected her. Humanity will die, but you protected her. Congratulations.
A winner is you.
