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. Written by Carl Lepeltier

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. Written by Claudio Carvalho, Rio de Janeiro, Brazil

A series of grotesque murder cases takes place on rainy days. Detective Hisashi Sawamura (Shun Oguri) works to catch the murderer like he has done with past cases, but he soon realizes the murderer's next target is his wife and son. A man in a frog mask is a suspect.

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. Written by Sonoda Haro, Kagoshima, Japan

Set in the late 21st century, an MRI scanner is introduced at the National Research Institute of Police Science's 9th Forensics Laboratory. The machine is able to scan the memories from even the deceased. As ethical questions arise over the machine's use, the 9th Forensics Laboratory members, including rookie Ikko Aoki and Chief Tsuyoshi Maki, struggle to solve cases.

Himura Kenshin is a legendary swordsman who has stopped killing people with his sword. Instead, he uses a dull-edged sword. He tries to live a peaceful life with Kaoru who runs a swordsmanship school in their village. Kenshin's past catches up to him causing the destruction of Akabeko Restaurant, which was Kenshin's favorite place to eat. There, he finds a note with the word 'Jinchuu' on it.

Kenshin Himura goes up against mysterious weapons dealer Enishi. He controls the underworld of China. The secret of Kenshin Himura’s "Jujishou" is also revealed.