After Act 2

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 Awaji campaign is a rebellion story as well as a rescue: the League inspires the island's people to rise against Yukari.

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. Yasuke's war against the Templars is personal. Nuno Caro killed his mother, and removing him is also an act of closure. Hanzo's confession shows that betrayal in this story is often driven by jealousy, not ideology.

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 side missions broaden the world: foreign traders, outlaws and ships show Japan's contacts with other regions.

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.

The Black Cross is an organisation within the Templars. Its members are inquisitors who hunt those who interfere with their search. The Observatory the Templars seek is the same Isu device from Black Flag, connecting Shadows to Edward Kenway's story.