I just finished my play through of the Last of Us, it is a great game with some amazing character development. I loved the main characters but I'm undecided if what Joel does at the end is the correct thing to do
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Yes. The Fireflies are a bunch of incompetent jerks who were willing to kill Ellie for a [i]chance[/i] at getting the cure. At no point is there a guarantee that a cure can be found. On top of that they are an activist group first and foremost; they would most likely have used it for their own goals rather than simply "saving the world."