Marlene's death is complicated because although she was somewhat of an antagonist to Joel, she had Ellie's best interests in mind when she made her decision to sacrifice her for the sake of a potential vaccine that could save humanity. Joel also discovered on a recorded audio file that the Fireflies would have gone along with the surgery regardless of what decision Marlene made, which makes it harder to see her as a villain as well. Though she is committed to her cause and fights for Ellie's death, it is for good reason and something Ellie would have probably wanted to do if she had a say in the matter. Joel's desperation for keeping his main source of emotional support drove him to kill Marlene when her death could have been avoided. After knowing Ellie her whole life and promising her mother she would keep her safe, Marlene is the one who has to do the opposite. Even though she begged for Joel not to kill her, it seemed like she was doing it more so she could hunt him down later on and retrieve Ellie for a vaccine once again. Whether Joel saw through it or not, he decided he didn't want her snooping around and killed her before she could even finish her sentence. It marks a time in the game where viewers don't know who the real bad guy is or if there is even one at all. The movie will need to highlight the fact that Marlene really had no choice but to sacrifice Ellie and that it wasn't personal though Joel felt differently.