The narrative arc features major shifts and revelations that culminate in the resolution of the Kyoto crisis:
- The Saito Infiltration: Saito's confrontation reveals that the Meiji Government is teetering on the edge due to Makoto Shishio's insurrection in Kyoto, forcing Kenshin out of retirement following Okubo's assassination.
- Aoshi's Fall to Darkness: Devastated by the death of his Oniwabanshu comrades, Aoshi Shinomori allies with Shishio solely for a rematch against Kenshin to bestow the title of the strongest upon his fallen comrades' graves.
- Mastering the Ultimate Secret (Ougi): In Kyoto, Kenshin reunites with his master Hiko Seijuro XIII to master Amakakeru Ryu no Hirameki. He learns that to wield absolute speed and power, he must abandon his subconscious death wish and possess a fierce will to survive.
- The Fall of Makoto Shishio: During the final battle, Kenshin, Saito, Sanosuke, and a redeemed Aoshi combine efforts against Shishio. Because Shishio's sweat glands were destroyed when he was burned alive, his body overheats beyond human limits during the extended duel, causing him to spontaneously combust and perish laughing in hellfire. Kenshin survives, fully reaffirming his choice to live and protect the new era with Kaoru and his companions.