I've spent a few hours considering where I think this franchise is likely to go for its third installment--which I believe is going to happen, and will be the final game in a trilogy.
If it were me telling this narrative, I think there are certain things that "must" happen to finish Ellie's story. From a storytelling standpoint, there are very basic things that "need" to happen in a third installment:
Humanity needs a path forward. Not necessarily a vaccine or immunity, but a path to beat back the cordyceps virus.
Ellie's life needs to have meant something. She needs to play some role in achieving a path forward for humanity. This does not mean she needs to die to make a cure--that would undo Joel's actions in Part 1. The older Ellie needs to take some sort of action that is crucial for humanity's path forward, and it needs to be something that only she can do.
Joel's decision to prevent Ellie's death and the development of a vaccine in Part 1 needs to have meant something. Joel knowingly snuffed out a chance for humanity to have a vaccine because he loved Ellie. This should narratively pay off in the form of the older, surviving Ellie being vital for the events in Part 3. Perhaps Part 3 begins with the Fireflies attempting a vaccine using another immune volunteer, only to learn it's impossible to synthesize. Ideally this should be handled in a way that makes it clear that Jerry, Abby's dad, was still right to believe he could make a vaccine from Ellie with the information he had.
Ellie needs to see that her life has mattered, thus allowing her to forgive Joel.
Not narratively required, but would be nice:
- Ellie gets to fly, realizing her childhood dream referenced in both parts 1 and 2. Perhaps she flies in service of whatever role she's playing to secure humanity's path forward. Perhaps as her final act.
Abby and Lev do not need to appear in Part 3, though they are wonderful characters. Dina and JJ do not need to appear in Part 3, though Ellie's abandonment of Dina does leave a gaping wound that could provide narrative fuel. Tommy does not need to appear in Part 3. Ellie does not need to survive part 3, and in fact she maybe shouldn't, given all of the horrible things she's done.