In 1866, after finishing sword training in Edo, Sakamoto Ryōma returns to his hometown in Tosa. After a scuffle with the Jōshi - the highest ranked of Japan's samurai - Ryōma is imprisoned and set to be executed, but is saved at the last moment by Yoshida Tōyō; Ryōma's father figure and a government minister who seeks to end the rigid social class system in Tosa.
Tōyō requests that Ryōma see his best friend Takechi Hanpeita, who has founded the Tosa Loyalist Party and also seeks to end the rigid social class system. Ryōma allies with Takechi, and the two formulate a plan: Takechi's forces will surround Kōchi Castle, while Tōyō will be inside negotiating with the ministers. As they are discussing the plan with Tōyō, an unknown assailant surprises the three. Using a style that Ryōma does not recognise, the assailant mortally wounds Tōyō, grievously wounds Takechi and easily bests Ryōma. Takechi survives, but Ryōma is forced to flee the pursuing security forces by jumping into the river.
One year later, Ryōma is in Kyoto, going by the alias Saitō Hajime. He discovers that the assailant who killed Tōyō was using a style called Tennen Rishin, which aims to be close to genuine fighting rather than sticking to any one style. It was practiced at the Shieikan dojo in Edo before it closed down, and its practitioners are now in Kyoto. After a run-in with the Shinsengumi, Ryōma meets an informant going by the alias Niibori Matsusuke, who reveals that all the practitioners of Tennen Rishin are in the Shinsengumi. Ryōma decides to join the Shinsengumi in order to get closer to the assailant.