A big part of The Last of Us is its last act, where Joel goes on a rampage and "selfishly dooms humanity" by saving Ellie. A lot of people think he was right, a lot of people don't, and some just think he's the worst, most selfish, kind of broken that a human can be. This whole discussion has bugged me since the game was released, and when I played it I found that the choices that Joel made were pretty much the same choices that I'd make as well.
First off, just to get this out of the way, it was never Ellie's choice to make. There's a reason that Ellie was knocked out when she cracked her head in the flooded tunnel and didn't wake up until the car ride out of Salt Lake City. The choice was only ever going to be between Joel and Marlene; save Ellie or save humanity, and Ellie was never going to get a say in this.
As for the Fireflies' whole plan, I think it's a pretty shitty plan all around and just to speed things up, I'll jot down why in a few bullet points.
They don't even know if they'll be able to make a vaccine from Ellie, they're just going to yank her brain out and give it a go.
A vaccine is fucking useless because who gives a shit if you're immune to the Cordyceps Virus when a Clicker is chewing out your goddamn jugular. There are still hundreds of millions of Infected roaming around the US alone, the few remaining survivors being immune won't change anything.
They didn't even ask Ellie what she wanted to do, they just found her unconscious and prepped her for surgery and went with the old "oh well, anybody would do the right thing and sacrifice themselves to save humanity" route of justification. It's an easy decision to make when you get all the benefits but don't have to make any kind of sacrifice.
Even if they could make a vaccine and even if they did manage to mass produce it - would they distribute it freely or try to use it as leverage against the military?
Now, you could say that Ellie wanted to make a difference, that she wanted her life to count for something, and you wouldn't be wrong. The problem with this is that throughout the mission through Salt Lake City, Ellie and Joel are discussing what they want to do after they've helped the Fireflies. Ellie specifically states that she'd like Joel to teach her how to swim and play the guitar. She's willing to help the Fireflies, but she's assuming she's going to survive the procedure. You don't go out and buy a week's worth of groceries and make dinner plans for next month if you're going to hang yourself later that day...
Now, Joel is just as much in the wrong as Marlene is for not waking up Ellie and letting her decide, but he's sort of got the moral high ground for not trying to kill a kid and harvest her bloody brain. Although I've got to say that even I agree with him on this one, who in their right mind would saddle that responsibility on a 14 year old kid? That's a recipe for instant survivors guilt and lifelong self loathing, so I've got no problem with Joel making the decision for her. If you're going to be making a decision for someone else, the very least you can do is chose the option that doesn't result in their death.
I should probably state that I think that Marlene is a piece of shit and I really don't like her. My main problem with her, among many, is that she thinks she's the good guy. She's been fighting the government for so long, on behalf of "the people," that she's gotten high off of her own bullshit. She actually recites the Firefly mantra in her journal, like a prayer, because she's starting to believe her own lies. She can justify killing soldiers who are only trying to keep people safe and apparently she's able to justify killing a kid she was meant to be looking after. She's so wrapped up in her own dogmatic ideology that any kind of violence, against any kind of target, is justifiable because it's in service of this non-existent group called "humanity."
The thing that really does it for me though, is that she begs for her life at the end. We don't get a defiant "you'll regret this" or a "you're dooming us all" line. No, all we get is, "Wait. Let me go. Please." There's not even the slightest hint of relief that Ellie is going to be okay, which you'd assume she'd have if the choice to sacrifice her had actually been that difficult to make. In her dying moments, Marlene shows us where her priorities truly lie - herself.
Marlene is a terrorist who started a war with the military, while they were protecting her from the Infected, because she couldn't live under their rules. And she's a piece of shit because she's willing to kill a kid to create a vaccine, just to further reduce the chances of her dying. Tess went out like a boss, Sam accepted his death and Henry willingly followed him, but Marlene went out begging like a coward. She's not brave and she didn't "make a tough call," she chose the option that would save "humanity" ie: herself.
Joel, on the other hand, is way down the other end of the spectrum. He's not willing to kill Ellie to save humanity, but he's totally willing to kill humanity to save Ellie. Which, if you think about it, is what you would do if you were a parent. Call me crazy, but if you're not willing to nuke a city to save your own kid, then you're not fit to be a parent. That's literally your only job, keep them alive, and you do that even if that means sacrificing your life or your soul. Marlene may have been watching over Ellie since she was born, but Joel was more a parent to her in that last year than Marlene ever was.
The hospital scene at the end causes some contention for a lot of people, because it seemed to outright change the goal of the game. Killing Fireflies suddenly seemed like a terrible act, since you'd been travelling to meet them for the entire game. But if you recall, Joel was never that friendly with the Fireflies, his brother even left them because they were getting a bit too crazy, and our first real encounter with them is when they blew up a goddamn truck in Boston. When did anyone ever say that they were the good guys? Joel's role as a guardian was to look after Ellie, which meant he protected her from any and all threats - even the Fireflies.
Now, you could state that killing the doctor at the end was a purely needless act, but if you go back and watch it again you'll see that it's otherwise. The only doctor you have to kill is the one that said "I won't let you take her." He then picked up a scalpel and pointed it at a guy who's clearly just slaughtered his way past dozens of soldiers... the doctor made a call to stand in your way and he doesn't let you pass unless you kill him. He doesn't even try to fight you, he's making you kill him. So you do. The other two aren't as resolute as him though, so whether or not you kill them is up to you. You, as in you the player, not Joel.
Also, I find it kind of hypocritical that the female doctor says that she doesn't want to die, when she was clearly about to butcher an innocent kid.
After that you go for a light jog, shoot Marlene in the face and then bail with Ellie. Once you get to the final act of the game you're playing as Ellie and you need to pass through a wooded area. To me, this just book-ended the game; you started as Sarah as she leaves the safety of home and you end as Ellie, as she journeys towards the safety of home. There's this bit in this last stage where Joel jumps up off a log to reach a ledge and the log falls down, so he has to reach down and pull Ellie up. I read this review that took this scene as a metaphor for toxic masculinity; where the selfishly ignorant male charges ahead, ruins the path, and forces the female to rely on the sexist male's aid to proceed.
This is exactly the sort of loaded interpretation that made me want to avoid the game in the first place. To me, this scene was simply a quick recap of the whole game, he took Ellie from civilization (the road) through the wilds (the journey) and then he carried her at the end (the ledge.) Ambiguity is the wiggle room that allows for interpretation though, so I'm sorry that my interpretation doesn't push forward some kind of socially progressive agenda...
Then there's the lie, the final aspect of the story that causes so much turmoil in the online community. I don't understand it really, because what else was he going to do? "Yeah, they could have saved humanity but you would have needed to die, so that's on you." No, fuck that - there's this insanely damaging thing called guilt that you really don't want to throw onto your kids if you can avoid it. Joel is Ellie's parent now, he needs to shield her from all this shit, because that's what parents do. They lie about Santa Claus, they lie about the gold fish dying, the lie about the bank foreclosing on the family home and they sure as hell lie when thousands of people will die in place of their kid.
I think it's entirely possible that Ellie knows, but at this point she's more interested in maintaining the relationship than digging for the truth. She knows Joel, she's spent a year trying to form a connection with this guy, and she finally got what she was after. Was it the perfect relationship? Hell no, but then it's a far from perfect world, even before the infection hit. Is she better off this way? Well, she's alive, and so is Joel, and she's going to live a few more years at least. Despite the demons she's no doubt accrued, it's still better than being dead.
I loved The Last of Us and I loved the ending, I felt that turning the Fireflies into the enemies you need to take out was a great twist. A few of them were still alive in the hospital as you left though, so they no doubt know what Joel and Ellie look like. I'm sure they'll be back in the sequel and feeling doubly justified in yanking out Ellie's brain.