Hey! I didn't comment in here.
I think that Joel saving Ellie was the right thing to do... kind of accidentally. Hold that thought.
The Fireflies are little more than a fairly inept terrorist group. They kept changing locations, losing men. They were falling apart before Joel even left on his journey, and they had fallen even further apart by the time he got Ellie to the hospital. Likely, they would only use the cure to try and gain some sort of power, power that they would soon find themselves in very little control over. That's if a cure could even be made.
Even if the Fireflies had totally good intentions and they managed to make a good cure, what then? They're going to start curing everyone? They're going to mass produce it? With what, exactly? The world is roaming with bandits and small pockets of people that barely resemble civilization. There's no way this "cure" is going to be mass produced. "The needs of the many outweigh the needs of the few" simply isn't relevant in this context because the few are being sacrificed for nothing at all, really.
Back to Joel doing the right thing accidentally - he would have saved her even if the above weren't issues at all. He needed to. It wasn't a rational action, it was an action from a basic human emotion of needing her.
As a final note, pay attention to the last few moments of the game. Not Joel lying to Ellie, the bigger picture that's ahead of them Joel's brother's village is growing. Earlier in the game, it was shown as the most civilized place you could be and might even be OK to live there if bandits weren't a constant problem. Humanity was learning to cope with the infection and it was building back up a little bit at a time. There was something worth living for and working for in that town. This world isn't completely gone without a cure, it's going to build itself back up. Not in Joel and Ellie's lifetime, but at some point humanity will be stable again.
EDIT: Also, the fact that the surgeon decided that Ellie had to be sacrificed so soon after getting her in there just screams "malpractice" and "incompetence". We're talking about an infection that no one knows anything about, here. Surely you don't want to kill your only live immune person?
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