I can definitely see why Joel did what he did. There was no guarantee that the operation on Ellie would have produced a vaccine, and there is always the possibility of other people being immune. Even if a vaccine is discovered, it won't fix everything. It'll need to be distributed, and there are countless infected who will still need to be killed.

He had been a broken man for 20 years and he finally found something to live for, and I don't blame him for not letting the Fireflies snatch it away from him.

Yeah it is very grey; but If you see the whole world as an ecosystem; if people really want to get through these hard times; people also need to work together instead of fighting with each other.  Just because the find some kind of vaccine wont make the whole world to be sugar and rainbows.  People kill, steal, and distrust each other; and a vaccine wont make that change.  Is people that needs to try to work together; and if they do; they will prevail; with vaccine or not.

Also there is no guarantee that the vaccine will work; first you need to do a medical trial in which you will require a lot of dudes with the vaccine to get exposed to the cordiceps; and if everything goes well; you might have your vaccine or it could be an EPIC fail.

The funny thing is that Ellie is not inmune; but it is the cordiceps in her mutated in a way that in does not kill the host.  So in reality they just need a bit of the fongus in her brain (in order to make it grow); and not the whole thing, which would kill her.

With my medical knowledge that is my point of view.  Maybe ND required a better epidemiologist/infectologist/medician as advisor;  OR I completely missed the point in those audio logs you find in the game ;).

I believe Joel didn't do the evil or the good thing, it isn't black and white, what he did do however, is the most human and realistic thing, which was to take Ellie back and lie to her to protect her and to ensure she doesnt feel guilty about the whole situation. He takes the guilt on himself, which is actually more admirable than him telling her the truth and having her bear the guilt aswell.

Now how do we all feel about Joel gunning down the Doctors and Marlene(who had put down her weapon). Not only did he take away their direct link to a cure but he also ruined their chance of making progress in another direction. Did he really need to kill them? A doctor has to be rare enough during an apocolypse that they should be treated as endangered species.

As for Marlene, she put down her weapon. She wanted to discuss the issue calmly and rationally. Joel wasn't having it and gunned her down. She was the leader of the Fireflies who acted as a beacon of hope for the people. She could have done much good. Does killing her assure that the Firefly remnants won't come after them? No, not really.

If Joel committed any crime, I think it was these two actions.