After Prologue

In this chapterAkechi Mitsuhide recruits Naoe, falsely identifying Nobunaga as the leader of the Shinbakufu.

Naoe tracks down and kills the first of the masked samurai. Akechi Mitsuhide offers her more targets and says that Nobunaga leads the Shinbakufu, the group behind her father's murder. At Honno-ji, Nobunaga reveals that Mitsuhide has lied. Nobunaga ends his life with Yasuke's help as Mitsuhide's forces close in.

The Honno-ji Incident is a real turning point in Japanese history, and the game uses it as the moment where the protagonists' paths meet. Mitsuhide uses Naoe as a weapon, which sets up her distrust of leaders and her desire to find who is actually responsible. Yasuke's assistance in Nobunaga's death is an act of loyalty, and it leaves him masterless.

In this chapterNaoe and Yasuke ally and form the Kakushiba ikki, the League of the Hidden Blade, with recruits including Tomiko and Junjiro.

Yasuke tells Naoe that he killed Momochi Sandayu, who gave him a message to help her. They form the League of the Hidden Blade, recruiting allies and hunting Shinbakufu members. At Yamazaki, Mitsuhide, dying, names Ashikaga Yoshiaki as the Shinbakufu's real leader. Yoshiaki gives up secrets to survive: the box contains an Imperial Regalia, and the Templars are supporting the Shinbakufu.

The conflict becomes a hunt for the Regalia and for the Templars who want them. The League of the Hidden Blade is the game's version of the Brotherhood: an alliance of outcasts, with each recruit adding skills and perspective. Yoshiaki's role shows how the old order tried to regain power by using foreign influence.

The Templars arrive from outside Japan, tying the story to the global conflict of the franchise.

In this chapterNaoe finds her mother Tsuyu's hideout and learns Tsuyu led the Brotherhood that guarded the Regalia until the Shinbakufu massacre.

Naoe finds the Assassin hideout of her mother Tsuyu, who led the group that protected the Regalia. Hanzo confesses his part in the betrayal and Naoe forgives him. Yasuke tracks down Templar operatives and finally faces Nuno Caro, who killed his mother, and he declares war on the Templars.

On Awaji Island, Kimura Yukari is holding Tsuyu. Naoe and Yasuke break her lieutenants, spark a rebellion and storm Iwaya Castle, where Yasuke defeats Yukari and Naoe rescues her mother. The mother-daughter reunion is the emotional centre of the game. Tsuyu was believed lost, and Naoe's father's death looks different once she knows the whole story.

Yasuke's fight with Yukari is also an argument about identity: she says he only follows other people's paths, and his answer is to choose his own. The decision to return the Regalia to the Emperor means the protagonists choose not to use the objects' power for themselves.

In this chapterThe Templars send the Black Cross inquisitor Sir Eamon Hathaway to kill them while he looks for the Observatory.

After collecting glyphs across Japan, Naoe and Yasuke open a vault in Wakasa that once belonged to Kassandra. The Templars send Sir Eamon Hathaway and Nirmala of the Black Cross to stop them and find the Observatory.

Yasuke is nearly killed, but recovers. In the end Nirmala dies and Hathaway is mortally wounded. Yasuke breaks the key to hide the vault, and Naoe keeps a crystal cube as a link to the Assassins. The vault connects Shadows to the oldest layers of the franchise, tying Japan to Odyssey's Greece and the Isu.

Yasuke's recovery hints at a hybrid nature, a link to the Isu that the game leaves open. Sealing the vault matches the League's philosophy: some knowledge is too dangerous to use.