You know what I would do for a The Last of Us Part 2? I'd make it a mixture of TLoU and Death Stranding.
You play as a marginally educated doctor of the US army, who because of lack of personel has to routinely go with soldiers to support them, while the better docs stay at the base.
Said base is stationed in an arid area of the USA, like Arizone or New Mexico. The game would be split in three acts, with the story as a whole being a climb out of the bottom of the barrel that is the apocalypse.
Part one would be the establishing of the new base, with the various characters being introduced and play-mechanics being shown. You travel between areas, scout places, contact towns similiar to Tommy's and convince them to rejoin the USA again, and contribute to creating functional roads between these areas.
Part two is where the story starts to roll, with new orders coming from the top brass (what is left of it) to collect people who demonstrated immunity to the cordycepts. The remaining fireflies spilled the beans of people like Ellie. Obviously the army wants to research that immunity and make it common. However, surviving holdouts of the Fireflies are now actively hunting immunes and murdering them to deny the military them out of spite. Complicating things are a cult that believes consuming immunes makes them immune in return, and Abbey being a serial killer of Joels.
Part three is the protag finding Joel and Ellie, or rather finding Tommy's village. You do favors for the villagers, you pitch your usual speech about how the people were once a part of a greater thing, you pass along advices and warnings from the millitary, and after a while Ellie comes forward to try and get more info about this whole "Would any immunes please help us defeat the cordicepts?" business. Eventually Joel and Ellie are convinced to come with you. That's where the gameplay makes a return to the first game, with three areas being dedicated to traveling back to civilization. That would be demonstrated by the first level being overgrown wilderness, the second one being gradually becoming more civilized, and the final being essentially a convoy on a functional street where you and Joel defend their transport against a bunch of desperate Fireflies.
The story ends with Joel and Ellie returning home after she donated some of her spinal fluid or something else, I'm a bit fuzzy on the details here, and they are greeted by Tommy asking how their journey was.
EDIT: So what do you all think?