Kenshin Himura goes up against pure evil Makoto Shishio who is attempting to overthrow the Meiji government. The fate of the country hangs in the balance as Kenshin Himura takes up the sword that he vowed to never draw again.

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.—Carl Lepeltier

The Chief of Police Hajime Saito and a team of policemen hunt down the outlaw Makoto Shishio, who was betrayed by the government after defeating the Tokugawa shogunate; however Shishio and his men slaughter the police officers and only Hajime survives. Kenshin Himura is summoned by the government to help them to find Shishio in Kyoto. He refuses first, but when a minister is murdered, he accepts to go and leaves the dojo of Kaoru Kamiya and the boy Yahiko Myojin, his friend Sanosuke Sagara and Dr. Megumi Takani. Kenshin meets the thief Makimachi Misao that tries to steal his sakabato on the way to Kyoto and they stumble upon a boy that tells that his brother and his parents are in danger. They find the trio murdered by Shishio's men and Kenshin defeats them in the nearby village. A man called Sojiro Seta contacts Kenshin and brings him to meet Shishio that asks Sojiro to duel Kenshin. Their sword fight stops when Kenshin's sakabato is broken and Shishio and his men go away. Meanwhile, Kaoru decides to find Kenshin in Kyoto and Yahiko and Sanosuke follow her. When Kenshin arrives at Kyoto, Misao asks whether he would like to go to a cheap inn. Kashiwazaki Nenji, who was the ninja Okina that worked for the Tokugawa shogunate, runs the place and teams up with Kenshin. He seeks out the talented blacksmith Shakku Arai to repair his sakabato and finds that he is dead. Arai's son Keiku does not help Kenshin, but when the evil Sawagejo Cho kidnaps his baby, he calls Kenshin to save his son and gives him a new sakabato. Kenshin defeats the Shishio's warrior and he is arrested by the police. Soon Hajime and Kenshin learn that Shishio intends to burn Kyoto down and they prepare the defense of the town. Is Sawagejo Cho telling the truth?—Claudio Carvalho, Rio de Janeiro, Brazil