The war against the Tokugawa Shogunate ended years ago. But there are some who are not happy with the outcome. Shigure Takimi watched his friends and family get slashed down in the name of freedom and prosperity. Now he and a band of desperate rebels have sworn to settle one final score. Only one man stands in their way: Kenshin Himura. But when Shigure discovers Kenshin's true identity as the Hitokiri Battousai, his fight becomes a personal vendetta.
Act 1 tells the story of how Kenshin came under the wing of Soujiro Hiko the 13th, and how Kenshin became a manslayer.
Act 2 details Kenshin's role in the revolution, how he met Tomoe, and how the rebellion was almost quelled.
Act 3 details how Kenshin lived with Tomoe and married her as a cover until his side replenished its forces to continue the rebellion.
Act 4 is about the betrayal against Kenshin, how he lived for the next few years as a manslayer, and the origin of his cross-shaped scar.
Kaoru goes to the harbor every day to see if Kenshin has returned. After a while, she starts looking back at her life with Kenshin and all the things that have happened.
Sano finds Kenshin and nurses him back to health just enough for him to get back home into Karou's arms. Meanwhile Yahiko teaches, Kenji, Kenshin's son, the value of being the son of a legendary samurai.
Told from the perspective of Misao Makimachi, this alternate retelling of the Kyoto arc chronicles the adventures of wandering swordsman Kenshin Himura and his quest in putting a stop to the evil Makoto Shishio and his plot to take over Japan.
Kenshin and Kaoru leave on a boat to visit a graveyard. In exchange for dinner, Sanosuke assists Megumi with the chopping of firewood. Yahiko is currently working at the Akabeko under Tae with Tsubame. Meanwhile, Kenshin and Kaoru spend the night at a local couple's house because of the rain.
In 1868, after the end of the Bakumatsu war, the former assassin Kenshin Himura promises to defend those in need without killing. Kenshin wanders through Japan with a reverse-edged sword during the transition of the samurai age to the New Age. When Kenshin helps the idealistic Kaoru Kamiya from the gangsters of the powerful opium drug lord Kanryuu Takeda that wants her school for his production of opium, Kaoru invites Kenshin to stay in the school. But the drug chemist Megumi Takani escapes from Kanryuu and seeks shelter in the school. Meanwhile the killer Battosai is murdering police officers and leaving messages attached to their bodies. When Kanryuu poisons the population to get the school, Kenshin and the street fighter Sanosuke Sagara join forces to attack their common enemy.
Makoto, an assassin who once was contracted by the government, has since become obsessed with tearing it down. Formerly, Kenshin was mainly concerned with protecting Kaoru, but the stakes are now higher as he struggles to protect the nation itself.
Kenshin wakes up to find himself at his master(Hiko Seijuro)'s house after getting washed by the waves to land while he was unconscious at sea for 3 days. Kenshin asks Seijuro to teach him the ultimate and pinnacle technique of the Hiten Mitsurugi school, the Amakakeru Ryu no Hirameki. Seijuro accepts Kenshin's request after they spar with each other. Meanwhile in Tokyo, Prime Minister Hirobumi Ito attends a meeting with Makoto Shishio who forces him to declare Kenshin a wanted outlaw and have him publicly executed or else Shishio will destroy both Tokyo and the government.
Similiar to the "Himura Kenshin's Greatest Hits" from the first special, this episode goes through every technique of the Hiten Mitsurugi Ryuu and explains how it works.
The episode mainly recaps and recollects the majority of Himura Kenshin's techniques of the Hiten Mitsurugi-ryū as a clip show with footage from past episodes, and describes in full each technique, bar the Soryusen: Ikazuchi, Hiryusen, or the Ryukansen and its Arashi and Kogarashi variants.