That’s roughly how I imagine a sequel. Moving the greater story forward by trying to use both Ellies and Abbys will to do something for the greater good of humanity. Some will call it character assassination, but I don’t give a shit. Naughty Dogs writing is good enough to keep me interested and the series need some kind of hopeful ending. Would be a nice trilogy with great themes that color each installment.Part 3 should be five years into the future and Ellie is a recluse living by herself in a town not far from Jackson like Bill. She is paranoid' alienated from everybody including Dina and JJ and does not trust anybody. Word gets back to her that Jackson suffers a terrible bandit attack so she goes back to see what she can do and she finds the town in shambles with only a few survivors. Some of those survivors are Tommy who has leaned to walk again but wears an eyepatch in his right eye and has closed himself off from everybody and Dina plus JJ.
Her and Tommy find out where the bandit camp is and they go to wipe it out and find a few people being held hostage. They free the hostages and one of them tells Ellie and Tommy about a doctor in Mexico who can develop a vaccine from immune people. without killing them so Ellie sees this as her chance to redeem herself and finally give her life some meaning. Tommy comes with her we see too broken people destroyed by vengeance and hate bond and rediscover their humanity through a greater purpose.
When they get to Mexico they find Abby involved with this group who are party of the newly formed Fireflies and Tommy wants to just kill her while Ellie realizes that though they will never be friends this is bigger than the both of them. She calms Tommy down and they develop this vaccine but realize it is a long way to rebuilding the world. Ellie and Tommy return and her Dina reconcile. The theme of the third game will be hope and will switch between Ellie and Tommy in gameplay. There could be SP Abby DLC if people want that.
We could also learn through notes what the origin of the outbreak is and the kind of human tinkering that made it jump from insects to people.