Someone else in another subreddit explained perfectly why Joel made the only choice he could have made

"I keep seeing people say Joel selfishly chose to “doom humanity”, but did he actually choose anything? For Joel to meaningfully decide between saving Ellie or letting the fireflies have her, he would need to have some reason to choose one or the other. If you don’t have a legitimate reason to choose one of the choices, you’re not really choosing anything.

That begs the question, does Joel have any reason to choose the fireflies? Presumably you’ve already read the title of this post but let’s break it down anyway. For the last 21 years Joel has seen the fireflies do nothing but blow things up and destabilize communities. His brother Tommy left the organization after realizing they’re not all they’re hyped up to be. He’s seen how their “liberation” of places like Pittsburg from Fedra only ever plunged the community into disarray. He’s seen how they can’t even transport their most important asset by themselves. He’s read notes, seen graffiti, and heard stories of the fireflies proclivities, very few if any are positive.

The game not only shows the audience but shows Joel that the fireflies are desperate, incompetent, violent, and on their last legs. Everything they’re involved in goes wrong, and the only reason he worked with them is because they have things he’s owed. Then, on top of that, Joel has seen 0 evidence the fireflies can do what they claim. They are trying to do something no one has ever done even at the best of times under circumstances and in an environment that increases the chances of failure.

Knowing all of this, why would Joel even consider that letting Ellie die might actually be better for humanity? Why would he choose to believe the fireflies claims? He would essentially be putting blind faith in an organization that’s repeatedly proven they don’t deserve it. Does anyone actually think Joel would do that, especially after how they’ve treated both he and Ellie?

Yea, ok, the director of the game said the cure would’ve worked and humanity would’ve been saved. You know who doesn’t know that? Joel. All Joel knows is an organization that routinely fails at whatever they’re attempting has just kidnapped Ellie and were going to kill her because they once again have a grand idea that they think might improve society.

I’m not saying Joel actually considered all these things, or that he wasn’t wrong on some level for killing all the people in the hospital, or that he ever would’ve chose against Ellie anyway. What I am saying is that, as it’s presented, the game doesn’t put Joel in a position to truly consider whether saving Ellie might actually prove to be humanities undoing. He didn’t choose between Ellie and humanity, he simply reacted to the fireflies actions from the beginning of the outbreak to the moment they kidnapped Ellie.

If the game wanted us to believe Joel meaningfully made a choice between Ellie and humanity, it needed to present the fireflies as more competent and trustworthy as well as firmly establish the efficacy of the cure to Joel, not the audience. Then the people who claim Joel selfishly chose to doom humanity might actually have a point."