[WARNING: Spoilers for Ghost of Tsushima's ending below]
It may take players a while before they reach the end of Ghost of Tsushima, but they will likely be surprised when they actually get there. While many players may assume the game ends with the elimination of Khotun Kahn and the eradication of his Mongolian forces, Ghost of Tsushima actually has one more important moment left.
Sucker Punch Productions' Ghost of Tsushima takes place on the island of Tsushima, a real-life location situated between Japan and the mainland. As the last remaining samurai on the island, it's up to players to step into the shoes of Jin Sakai and become the titular Ghost of Tsushima, a dangerous force who will stop at nothing to rid the Mongolians from his lands and free his people.
It's this journey towards becoming the actual Ghost of Tsushima that encompasses most of the emotional arc of Ghost of Tsushima, and the way Jin handles his newfound approach to violence is tested over and over again throughout the course of the game. While his new friends like Yuna and Taka may tell him there is no other option, Jin's upbringing at the hands of his uncle, Lord Shimura, tells him differently.
Ghost of Tsushima's Final Duel
The final battle in Ghost of Tsushima is not against Khotun Kahn or any of the other Mongolian warlords. Instead, players must face off against their uncle, Lord Shimura himself, who has been tasked by the Shogun to kill Jin for the war crimes he has committed. Lord Shimura taught Jin to always look his enemies in the eye, to never strike from the shadows, and to always be as honorable as possible. However, by the end of Ghost of Tsushima, Jin has had to perform numerous dishonorable and murderous things.
Although he is conflicted about his own actions, Jin does not believe what he did was necessarily wrong, especially because he only took such extreme measures in order to ensure that no harm would befall the people of Tsushima. His uncle cannot see things his way, however, and neither can the leader of Japan, who has called for Jin's execution. After sitting down to write poetry together one last time, Jin and his uncle face off for Ghost of Tsushima's final story duel.
After defeating Lord Shimura, the player has the option to either kill their uncle or offer him mercy. Whichever option the player chooses has no bearing on the overall flow of the game (either way, the story is over and players are free to explore the open world at their leisure) but it is up to them as to whether Jin offers his father figure another chance at life or not. While some players may worry that leaving Lord Shimura alive may cause futher complications down the road for Jin, this does not seem to be the case, and either way the Ghost will always be a hunted man on the island of Tsushima thanks to the Shogun's decree.
At the end of Ghost of Tsushima's story Jin is a wanted man, hunted by the shogun and the Mongols alike, but he is also the savior of the people of Tsushima. Much like Batman, he may not ever get the glory and rewards he deserves from the government, but the people he serves know how integral the Ghost of Tsushima was in securing their freedom.