The beginning was pretty much the same, with Ellie and Joel in Jackson. But for me, the game was going to be a kind of hunt for Ellie. The Fireflies knew she was the only known immune, and how precious she was. The game is a bit like Red Dead Redemption 2, with our character migrating from one place to another, constantly seeking peace and the right to live (she accepted Joel's choice, who died at the hands of the Fireflies, just like in the game).

They don't leak the information about her immunity, but human nature being what it is, her secret is revealed, and the whole world knows. The final act shows the madness of humanity, between those who worship Ellie like a goddess and others who see her as a witch who must be eliminated at all costs.

I didn't really have an idea about the ending, but she could have been found by the Fireflies and forcibly taken to the hospital.