Before cutting back to Ellie and Joel, we watch Marlene fulfill Anna’s dying wishes: to watch over Ellie, and to shoot Anna before she turns into an infected. Finally, viewers of the show have some context as to why Marlene had been watching over Ellie and enrolled her into FEDRA boarding school. While Marlene was out being a revolutionary, Ellie would be safer in a place the Fireflies would never attack.
Marlene doesn’t have as much of a presence as Joel in the long term narrative of “The Last of Us,” but when it comes to the ending’s moral dilemma (which changes the entire context of the story), her role, especially as Joel’s direct character foil, is just as significant. As Ellie is unconscious and is getting prepped for a fatal surgery that could reverse-engineer a cure, Joel claims that she doesn’t know what’s at stake. In the game, Marlene makes subtle references that she knows exactly how Joel feels, but the player never gets the full extent of what she means unless they engage with optional voice recordings and diary collectibles throughout the final level. Thanks to the additional cold open in the HBO adaptation, we know exactly what Marlene means — in fact, as Ellie’s distant guardian, we’re shown, not told, that she may be the only one who truly understands Joel’s pain.
At the end of the day, Marlene is an incredibly principled character and is fully devoted to her cause to restore what’s left of society. To her, the needs of the many outweigh the few. Despite what Joel thinks of her at this moment, her choice to sacrifice Ellie in pursuit of a cure is not something that’s easy for her.