The year is 1274, and the Mongol Empire has arrived on Tsushima to prepare for an invasion of mainland Japan. Players are introduced to samurai Jin Sakai, along with his uncle, Lord Shimura, jito of Tsushima, who are now marching into battle against an overwhelming force. In an attempt to prevent a large battle with the enemy, Lord Shimura sends his second-in-command, Lord Harunobu Adachi to confront the Mongol Soldiers on the beach of Komoda.
Lord Adachi challenges the Mongols to send their finest warrior to fight him, and Khotun Khan, the leader of the Mongol forces, steps forward. The Khan throws alcohol on Lord Adachi, sets him on fire, then decapitates the commander. Khotun Khan demands the samurai to surrender, but Lord Shimura, angered by the dishonorable tactics of the Khan, stands his ground and attacks with the full force of his eighty (80) samurai. Despite Jin's and Shimura's efforts, however, Tsushima suffers a devastating defeat as nearly all samurai are killed by the Mongol enemies. As Jin and Shimura charge towards the Khan, they are knocked back by a projectile. Jin wakes up among a field of dead samurai bodies, and notices that his uncle has been captured by the Mongols. Jin tries to go towards his uncle, but is shot down by archers. The Khan captures Shimura, and asks him to surrender. Upon Shimura's refusal, the Khan knocks him out with the hilt of his sword.
Jin wakes up without his armor and weapons, and witnesses Mongols torturing and killing villagers in a nearby village. He sneaks around the village and enters a house, where he notices his now-broken armor. He exits the house, before being pushed back inside by a villager who asks how his wounds are. Jin is confused, but hides as a Mongol soldier interrogates the villager for rice. The villager feigns fear and allows the Mongol to search for rice, before stabbing the soldier multiple times from behind. Jin is repulsed by such tactics; he asks who the villager is, who introduces herself as Yuna. She tells Jin that if he wants his blade back, he should follow her.
The two sneak around the village, witnessing the violent acts of the Mongols against the civilians along the way. Yuna ensures Jin that Shimura is still alive and is being held somewhere in the east. As Yuna and Jin move along rooftops, Jin questions Yuna's methods; Yuna says that she does what she needs to, including selling Jin's katana for food and medicine. They collect supplies, and eventually reach the buyer's house, where the buyer is dead. Jin finds his katana, and remembers his training with Shimura when he was younger.
After reflecting on his training, Jin kills a Mongol spearman with his blade. Yuna and Jin then go to the nearby stable, only to find Mongols guarding it. Yuna suggests that they sneak up behind the Mongols and slit their throats, but Jin advises against it, as it is dishonorable, and they should instead face the Mongols head-on. Yuna and Jin dispatch the Mongols, saving a villager, Kiheiji. As Jin reflects on why he saves people, Yuna notes that her brother, Taka, was taken by the Mongols, making Jin realize why Yuna had healed him in the first place. Jin ensures that he will save Taka after he frees Shimura from the Khan.
Jin and Yuna kill a few more Mongols, and then arrive at the horses. After Jin decides the color and name of his horse, the two travel to Castle Kaneda. Jin insists on going into the castle alone. After dispatching many enemies along the way, he arrives at the bridge leading to the castle proper, where Khotun Khan is waiting. Jin and the Khan duel each other, with the Khan easily besting Jin and throwing him off the bridge into the waters below. As Jin is unconscious, he reflects on how he was not able to save his father from dying to bandits, and how he honored his father with various people, including the family caretaker Yuriko and Sadanobu Ishikawa. Shimura tells Jin that he must carry on his father's legacy, and that he will continue to train under Shimura's care.
Jin wakes up on the beach, and follows the wind to his steed, and also finds Yuna and her steed. Jin explains to Yuna what happened, and Yuna vows that she will not leave Jin's side until her brother, one of the island's best blacksmiths, is saved. Jin states that he needs to find more allies, such as Ishikawa and Masako Adachi. Jin asks Yuna to check around Kechi, and will join her soon, before the two separate and Jin rides his horse through the fields, opening up Act 1: Rescue Lord Shimura.
The Mongol Empire is invading our home. They are brutal. Relentless. Unstoppable. We are eighty samurai against an army. Fighting to slow the invasion. Today... I die for my people.
― Jin
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Kiheiji Seen Again
Kiheiji has a short conversation with Jin.
Much later after the player's release into the open world, Kiheiji, the peasant that Jin and Yuna saved, can be seen again in the Golden Temple. He holds a short conversation with Jin.
Khotun cannot be defeated in the encounter at Castle Kaneda, as his health is artificially made to never drop to zero.
