When Uncharted 4: A Thief’s End was originally conceived, it was supposed to be written by Amy Hennig. It looks like her story for the game was completely scrapped in favor of a new one.
Early in the game’s development, Uncharted 4: A Thief’s End was being managed by a different Naughty Dog team. Amy Hennig was the head writer and people like Alan Tudyk were cast in the game.
Things changed however after the success of The Last of Us and Neil Druckmann with Bruce Straley took over. Amy Henning left Naughty Dog to work on a new Star Wars game while Alan Tudyk and other actors were cut. Druckmann and Straley brought over Troy Baker, Laura Bailey and other actors to work on the game instead.
Druckmann and Straley confirmed that Uncharted 4: A Thief’s End’s story was reworked completely during an interview with the New York Times. They confirmed that the story was changed “100 percent” with all new writers. This is similar to how George Lucas pitched ideas for The Force Awakens, but Disney turned them all down.
The reason they wanted to rework the story was because they knew this would be the last Uncharted video game. They wanted the Nathan Drake character to go out with a bang so the series would end on a high note.