In 1274, Jin Sakai and his uncle, Lord Shimura, jitō of Tsushima island, lead the samurai garrison of Tsushima into battle against an invasion fleet from the Mongol Empire. The battle is a one-sided massacre; the samurai are overwhelmed by the enemy's sheer weight of numbers, Jin is wounded and left for dead, while Shimura is taken prisoner by the Mongol leader, Khotun Khan. Yuna, a woman thief, recovers Jin from the battlefield and nurses him back to health, informing Jin that the Mongols have already conquered most of the island during his convalesence. Jin launches a one-man attack on Castle Kaneda, which the Mongols have seized as their base of operations, in a desperate bid to free a captive Shimura, but he is easily overpowered in a duel with Khotun and flung from a bridge.
Though Jin survives the fall, he is left humbled by his defeat; realising that conventional tactics and adherence to bushido will not defeat the Mongols, Jin gathers a number of allies, including Yuna, her blacksmith brother Taka, master archer Sadanobu Ishikawa, the warrior woman Lady Masako Adachi, travelling merchant Kenji, and his old friend and leader of the Straw Hat rōnin, Ryuzo, with the intention of retaking Castle Kaneda and freeing Lord Shimura to co-ordinate efforts to repel the invaders. As Jin's efforts to disrupt the Mongol invasion gain him notoriety, the people begin to refer to him as "the Ghost", believing him a vengeful samurai spirit returned from the dead to punish the Mongols, stories encouraged by Yuna. After gathering his allies, Jin scales the walls of Castle Kaneda with a grappling hook forged by Taka, before opening the castle gates to allow his allies to storm the fortress. Destitute and starving, Ryuzo and the Straw Hats betray Jin, hoping to claim the bounty Khotun put on his head, but Jin fights them off, before he and his remaining allies free Shimura and retake Castle Kaneda from the Mongols. Despite their victory, Ryuzo escapes to join Khotun, who has already marched north to conquer Shimura's ancestral castle.
Needing a new army to retake Castle Shimura from the Mongols, Shimura dispatches Jin to recruit new allies, including the warrior monks of Cedar Temple and the warriors of Clan Yarikawa. Despite the bad blood between Yarikawa and Shimura after the latter bloodily put down a rebellion by Clan Yarikawa decades earlier, Jin convinces Yarikawa's lord to ally with him after breaking the Mongol siege of their fortress. Shimura also dispatches a petition for reinforcements to the shogun, along with a request to formally adopt Jin as his heir. Jin also returns to his home of Omi village in the north of Tsushima and reclaims his family's ancestral armour from his estate's caretaker, Yuriko, who also teaches him poisons to use against the Mongols. With Ryuzo and the Straw Hats threatening Shimura's flank, Jin is dispatched to infiltrate a fortress the Straw Hats are occupying to eliminate them, but he is taken captive, along with Taka when the latter tries to free him. Khotun tries to force Jin to join him in a bid to coerce the population of Tsushima into surrendering to the Mongol Empire; when Jin refuses, Khotun kills Taka in retaliation. Yuna infiltrates the fortress, frees Jin and helps him eradicate the Straw Hats, though Ryuzo escapes again, before burying Taka's body. Reinforcements from the shogun arrive to augment the army Jin and Shimura have assembled, and Shimura leads an all-out attack on Castle Shimura's Mongol occupiers. Despite making initial gains, the Mongols retreat to the keep and destroy the bridge with improvised explosives, inflicting enormous casualties on the attacking samurai.
Realising another frontal attack will only guarantee more lives lost, Jin opts to infiltrate the castle and poison the Mongols' supplies of food and drink. He also encounters and kills Ryuzo in a final duel when the latter refuses to surrender; a dying Ryuzo informs Jin that Khotun has already left for the far north of the island. Despite the bloodless victory, Shimura is appalled by Jin's actions, since using poison goes against the samurai's code. Aware that the shogun will want someone executed for these actions, Shimura begs Jin to make Yuna a scapegoat for the Ghost's atrocities and accept the shogun's offer to formally name Jin as the heir to Clan Shimura; Jin refuses, embracing his identity as the Ghost and is arrested, but manages to escape. Reuniting with Yuna, Jin learns that Khotun has worked out how to duplicate the poison he used, and the Mongols plan to use it for biological warfare against the Japanese mainland. With the Mongol fleet trapped in port by an approaching storm, Jin gathers his allies for a final attack on Khotun's last stronghold, as well as sending a letter to his uncle, pleading with Shimura to bring samurai reinforcements to overwhelm the Mongol defenders. In the ensuing battle, Jin duels Khotun one final time, killing the khan aboard the deck of his burning flagship.
The Khan's death robs the Mongols of their momentum and allows the samurai to turn the tide against the invaders. In the aftermath of the battle, Shimura confronts Jin, informing him that the shogun, fearing Jin's actions as the Ghost threaten the status quo and could incite an uprising against the samurai, has disbanded Clan Sakai and ordered Shimura to kill his nephew. The pair spend a final afternoon in each other's company before engaging in a duel to the death; emerging victorious, Jin then decides whether to give his uncle a warrior's death in accordance with Shimura's wishes, or to spare his life and walk away. Whatever Jin decides, he departs and goes into hiding to avoid the shogun's supporters, while covertly helping his allies deal with the last remnants of the Mongol invasion.
Iki Island
Some time after the confrontation with his uncle, Jin finds a community of villagers who've been attacked and poisoned by a raiding warband of Mongols unlike those he has encountered before. The Mongols fight under the command of Ankhsar Khatun, a warrior shaman known to her followers as "The Eagle", who are, as Jin discovers, attempting to conquer Iki Island, a small island close to Tsushima. Jin is reluctant to head there, as the island holds grim significance for him; twenty years earlier, his father, Kazumasa Sakai led a brutal campaign at Shimura's behest to suppress the pirates and raiders assaulting Tsushima from Iki. Jin was present during the campaign, and witnessed his father's death in battle against the raiders, something that still haunts him as Jin was too afraid to try and save his father. Despite his misgivings, Jin recognises the Eagle and her followers have to be stopped and sets sail for Iki.
Jin is shipwrecked on Iki, and his attempts to infiltrate the Mongol stronghold at his father's old base of operations, Fort Sakai, ends with him being captured by the Eagle's second-in-command, Khunbish. The Eagle forcefeeds Jin the same poison she used on Tsushima, causing him to hallucinate visions of his father's death and other failures; the Eagle tries to convince him to join her and finish his father's work in conquering Iki, but Jin refuses and escapes. He's found in a delirious state by Tenzo, one of the native raiders of Iki, who grudgingly brings him to Fune, leader of the raiders, though Jin hides his true identity out of fear of their reaction. Despite their distaste for the samurai due to the atrocties Kazumasa committed on Iki, Jin slowly earns their trust by helping break the Mongols' hold on the island, culminating in the raiders aiding him in an attack on Fort Sakai that ends with Khunbish's death. In the aftermath of the battle, Jin witnesses Tenzo dispatch a mortally wounded Mongol with the words "May your death benefit all beings", the same phrase his father's killer spoke before striking the deathblow. A furious Jin confronts Tenzo for hiding this from him, but forgoes vengeance, knowing that killing Tenzo would shatter the fragile alliance between him and the raiders, and that the Eagle is a far greater threat, as well as having seen during his travels that the people of Iki had genuine reason to hate his father.
Jin proposes replicating the ambush in which his father was killed to draw out and assassinate the Eagle. In the ensuing battle, the hallucinations inflicted on him by her concoction nearly overcome Jin, and he is forced into a final confrontation with a spectre of his father. Jin overcomes the effects of the poison by accepting his father's flaws and letting go of his guilt over his father's death, saving Tenzo from a killing blow from the Eagle and slaying her in a duel. With the Eagle's death, the Mongols' hold on Iki crumbles, while Jin and Tenzo part ways amicably, both men having come to forgive the other.
