Most likely, Ellie will become a focus character in the third game, like Joel was in TLOUP2. Everything that happened was because of him. Everything was linked to him. The same will happen to Ellie and new protagonists are going to be introduced.
To all the geniuses here making a novel out of this, you don't need to like a character to enjoy the story. Go take a look at the Night of the Living Dead. You are going to understand that this game has the same vibe behind it. It is a message against our liberal society. We talk about freedom but we cannot even accept someone else difference.
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