In The Last of Us Remastered's commentary with director Neil Druckmann, he stated that there was originally going to be dark music during the scene when Marlene revealed that Ellie was going to be sacrifice for a cure. However, Druckmann told the composers not to do that, because it would paint her as a bad person rather than a good person who is trying to save humanity. Instead, he let them use the dark music for Joel, because when Ellie's life is on the line, he slips back into murdering anyone who would try to kill her. Neil also stated that this scene defined the theme of the game: "as a father... you will... kill everybody else to save your kid."
Contributed by ProtoSnake