Being embroiled in the middle of a Tosa coup d'état and bent on finding the murderer who assassinated his father figure, Ryōma burrows himself with a hidden identity in the streets of Kyo and joins the grim Shinsengumi.

Players control the sole playable protagonist, Sakamoto Ryōma, and have access to a total of four fighting styles: Swordsman (which uses a katana as the primary weapon), Gunman (which uses pistols), Brawler (which uses hand-to-hand combat, more similar to the traditional combat style), and Wild Dancer (which uses a combination of katana and pistol).

Japan is thrown into turmoil after the arrival of Western ships, galvanizing the imperialist ideals of the Shishi, who wish to rebuild the nation around the Emperor by overthrowing the Bakufu and expelling foreigners.

The primary protagonist of the game is Sakamoto Ryōma (Takaya Kuroda), a disgraced rōnin from Tosa who seeks to avenge his murdered adoptive father, Yoshida Tōyō (Unshō Ishizuka).

Escaping to Kyo as a wanted man, Ryōma joins the Shinsengumi using the alias Saitō Hajime, in order to track down Tōyō's murderer.

Notable members of the Shinsengumi include: Chief Kondō Isami (Eiichiro Funakoshi/Akio Otsuka), Deputy Chief Hijikata Toshizō (Nakamura Shidō II), Military Advisor Itō Kashitarō (George Takahashi/Hitoshi Ozawa), Inspector Yamazaki Susumu (Nobutoshi Canna/Yuichi Nakamura), and the Division Captains: Okita Sōji (Hidenari Ugaki), Nagakura Shinpachi (Rikiya Koyama), Matsubara Chūji (Hiroki Tōchi), Takeda Kanryūsai (Shun Sugata/Riki Takeuchi), Inoue Genzaburō (Shunsuke Sakuya), Tani Sanjūrō (Kenji Hamada/Masanori Takeda), Tōdō Heisuke (Shunsuke Daito/Nobuhiko Okamoto), Suzuki Mikisaburō (Ryōta Takeuchi/Ayumi Tanida), and Harada Sanosuke (Hiroki Yasumoto).

Ryōma is also supported by other allies, including: Katsura Kogorō (Koichi Yamadera), leader of the Chōshū Loyalist Party; Saigō Kichinosuke (Masami Iwasaki), General Commander of the Satsuma Domain Army; Nakaoka Shintarō (Kazuhiro Yamaji), Tōyō's former retainer who cooperates with Ryōma to investigate Tōyō's death; Otose (Romi Park), the proprietor of Teradaya Inn where Ryōma stays at during his time in Kyo; Oryō (Nanami Sakuraba/Manami Sugihara), a young woman who works at Teradaya as Otose's apprentice; the Bathkeeper of Sai (Yoshiaki Fujiwara), a renowned information broker in Kyo; and Ikumatsu (Aya Hirano), a geisha who operates as a spy for the Chōshū Loyalist Party.

is Takechi Hanpeita (Katsunori Takahashi/Hideo Nakano), Ryōma's sworn brother who commands the Tosa Loyalist Party following Tōyō's death.

Other antagonists include: Sasaki Tadasaburō (Rintarō Nishi), commander of the shogunate police force Mimawarigumi; Katsu Rintarō (Kenyu Horiuchi/Kohsuke Toriumi), Admiral of the Bakufu Navy; Tokugawa Yoshinobu (Satoshi Tokushige), the 15th Shogun of the Tokugawa clan; and Yamauchi Yōdō (Hiroaki Yoshida), the ruthless daimyo of the Tosa Domain.

In 1866, after finishing sword training in Edo, Sakamoto Ryōma returns to his hometown in Tosa and reunites with his adoptive father, Yoshida Tōyō, and his sworn brother, Takechi Hanpeita.

Having been accused of murdering Tōyō, Ryōma escapes captivity, vowing to return to Tosa to prove his innocence once he captures the assassin.

After encountering an individual who calls himself Niibori Matsusuke, Ryōma is introduced to the Bathkeeper of Sai, an information broker who reveals to him that the Tennen Rishin style is practiced by the founders of the Shinsengumi.

In one of his first assignments, Ryōma accompanies several Shinsengumi captains to apprehend Okada Izō, Takechi's right-hand man who has gained notoriety for assassinating several Bakufu leaders.

Ryōma eventually learns that there is an imposter using his name, who has been making arms deals with the British, with the backing of Navy Admiral Katsu Rintarō.

First Division Captain Okita Sōji, who overheard the conversation, later challenges Ryōma to a fight while pretending to be the killer, and ultimately loses.

In a drunken state of depression, Ryōma manages to stop a scuffle between Katsura and Saigō, allowing the two of them to befriend one another and end their ancestral feud.

Okita accuses Ryōma of having carried out the murder, but Kondō intervenes and reveals the truth: Inoue, whose true identity was Serizawa Kamo, was hired by Ryōma's imposter to assassinate Tōyō a year prior; he, alongside his fellow exiled Mito comrades Hirayama Gorō and Hirama Jūsuke, was targeted by the real Okita, Inoue and Nagakura, but Serizawa killed them in self-defense.

Kondō and Hijikata agreed to keep this event a secret, and had Serizawa, Hirayama and Hirama take up the identities of Inoue, Okita and Nagakura, while also passing down their fighting technique to other Shinsengumi captains as the Tennen Rishin style.

Ryōma later reports to Kondō and learns that Katsura and Saigō have united their armies to form the Satchō Alliance, as they prepare to wage war with the Bakufu.

In his final breath, Izō confirms that Takechi has been posing as Ryōma as part of his plot to ignite a war between the Emperor and the Bakufu.

The next day, Hijikata summons the remaining Shinsengumi captains and exposes Military Advisor Itō Kashitarō for his complicity in Kondō's death.

Itō, alongside captains Takeda Kanryūsai and Tōdō Heisuke, announce their defection as they form a new organization, the Goryo Eji, comprising a large number of Shinsengumi troops.

[3] On February 22, 2014, a 200KB DLC named Digest Narration Voice (ダイジェストナレーションボイス) was made available on the Japanese PlayStation Store priced at ¥300.

[32] Polygon praised the game's depiction of 19th century Kyoto, writing, "The environments are gorgeously rendered, with unpaved roads punctuated by maple trees and streams that run through the city".