The game depicts the leadup to the Boshin war between the Tokugawa Shogunate and various anti-shogunate factions displeased with the western influence after the forced reopening of Japan following the Sakoku period.

[4][7][8] The story follows the Blade Twins, whose genders are selected by the player, and their involvement in the Veiled Edge resistance group after their family was murdered by oniwaban working for the Shogunate.

In the year 1853, the Blade Twins are tasked by the Bladesmith to assassinate Commodore Matthew Perry and steal a secret message in his possession.

The social order of Yokohama and all of Japan has been thrown into turmoil due to the arrival of the Perry Expedition and increasing Western influence in the country.

As Ryoma searches for his master Shoin Yoshida with his fellow students, the Protagonist investigates the whereabouts of their partner, now known as Demonclaw Samurai, who is working for the Americans and British.

Shogunate Chief Minister Naosuke Ii enacts harsh suppression and purges of anti-Shogunate and anti-foreigner sentiment, culminating in Shoin's arrest and execution in 1859 which angers Ryoma and his friends.

The Protagonist and Ryoma attack Katsu, who easily fights them off and instead wins them to his side by telling them his desire to reform the Shogunate and modernize Japan without the use of violence.

However, shortly after their arrival in Kyoto in 1864, the leader of the Roshigumi, Kiyokawa Hachirō, is assassinated by the Demonclaw Samurai and exposed as a traitor, throwing the organization in chaos.

In 1867, despite Yoshinobu engaging in negotiations with the Choshu-Satsuma alliance, the Demonclaw Samurai begins to stage false flag attacks to stoke tensions between the two sides, culminating in them attempting to assassinate Ryoma, who envisions a Japan under democratic rule.

Katsu makes plans to burn down Edo to prevent its capture, but the Protagonist is able to negotiate a peaceful settlement between the two sides that spares the city.

If the player manages to save Ryoma's life and spares the Demonclaw Samurai, a post-credits cutscene shows the two of them running into each other in New York City.

Yasuda cited creating passive non-player characters as "impactful" and "challenging", as in their previous titles everything on-screen was for the player to defeat.

[10] Commenting on his work, Ōtomo stated he wanted to show the buildup of energy in the darkest moments of the Bakumatsu, as the people "waited for everything to implode".

[10] He took it upon himself to study Japanese music as part of the job[12] and felt that writing the theme for the Blade Twin was the most challenging, noting that their actions were not purely good or evil, but considered to be "different" and contradicting the story of the protagonist.

Early reports indicated that this is due to comments by Fumihiko Yasuda comparing Shoin Yoshida to Socrates, which sparked controversy in South Korea.

Although Yoshida played a key role in the Meiji Restoration, he is also considered an integral person in what would lead Japan to conquer and occupy Korea.