Okina says the writing is either Portuguese or Dutch, and the symbol on the bottom of the letter was the same symbol carved into the body of the murdered man. Kenshin decides to help the woman by defeating the man quickly and Karou discovers that Kenshin is actually the Battosai. Elsten was interfering too much so Santo tried to kill him but Magdaria jumped in and was shot. Cho tells Kenshin that Amakusa is better than Kenshin. It has already start and the water clan has attacked the dojo now the dojo and the restaurant is no longer needed and the formation has already begun. His late wife's brother decides to seek out revenge for the death of his sister which he blames on Kenshin and kidnaps Karou leaving behind something that looks similar to Karou for Kenshin to grieve over. Tetsuma try to reason why Katsu but it wasn't enough then he tried to fight him but Kenshin stepped in.
They got on to the boat and set sail to return back home. A hunter appeared and brought Yahiko in and treated him, he gave Kenshin some more clues as to where the divine medicine was, Yahiko got better and they left. 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. Kashiwazaki Nenji, who was the ninja Okina that worked for the Tokugawa shogunate, runs the place and teams up with Kenshin. The Kenshin-gumi go to the ambassador's residence for tea and crumpets. Kaoru screamed and didn't know what to do, the kitchen was on fire, Kenshin sensed something was wrong and asked where Itsuko was, he went out side and found her hair pin on the ground.
As it turns out, Prince Shin looks exactly like Yahiko, and so Yahiko is put in his place to attend a banquet. Back at Katsu's home, Tetsuma was caught, Katsu knew it was him looking for the map to the hidden money. Their sword fight stops when Kenshin's sakabato is broken and Shishio and his men go away. Sanosuke and Shouzo show up and were trying to stop Kaiou but got locked into the cage with Magdaria, to make matters worse an explosion occurred and rocks were falling down on them. An official arrives and tells them that the believers can no longer stay in Japan, Elsten is thankful for the decision and decides that the believers can come to his country, Holland. After achieving many obstacles Sanosuke finds some luck and sees Elsten. 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.
He defeats Cho and then kills the man he came to kill. It was hard to understand so Sanosuke and his friend went to find the author and he explained everything. Soon after Kenshin, Kaoru, Yahiko and Kenshin leave and gets caught by someone. Kenshin had already started to fight Shougo, finally both used the succession technique and Shougo was defeated. Omasu, Ochika and Aoshi arrive and are ready to take Misao back to Kyoto. Kenshin visited Elsten to find out what will happen to the believers and so on. Aoshi refuses, but Misao sees the letter and takes it to Okina.
He shows Kenshin the map and tells him that his clan had an Eigou formation that would protect the town, the water clan also wanted a formation but the both would conflict, so they tried to destroy the Eigou formation. Kenshin and the rest are looking for a place to stay but they were all full, they make their way up to the fake Battousai's place and sees he's running a dojo. The boat arrived back in Tokyo and everyone was waiting for Kenshin and Kaoru to get back. After each of these incidents, a man claiming to be a Feng Shui master appears to provide advice to the victims. Meanwhile Sanosuke took a long bath and Megumi washed his clothes and he was forced to wear something else, soon everyone went to sleep. Sanosuke and his friend went looking around for clues, finally they got possession of a book that gave many useful clues. Though he makes a life for himself here in his new home he also attracts many enemies from the past and new enemies as well.
Magdaria and Shougo are traveling by carriage, then boat to Shimabara. When the Akobeko catches fire from one of its stoves, Tae and Tsubame go to live at the Kamiya dojo, where they are attacked by Feng Shui fledglings following a visit from the entrepreneur, whose services Tae refused. Meanwhile, Kaoru decides to find Kenshin in Kyoto and Yahiko and Sanosuke follow her. Meanwhile Sanosuke gives Kaoru a letter and she makes a visit to Shougo. Daigoro continues to train and has a match with Yahiko.
Daigoro's teacher than kicked him out of his dojo since he wasn't very good with a sword. Meanwhile the killer Battosai is murdering police officers and leaving messages attached to their bodies. Kenshin has settled into his new life with Kaoru and his other friends when he is approached with a request from the Meiji government. Then a man claiming to be the legendary Battousai arrives and scares them away. Sanosuke found Kenshin and Jinpu and explained everything, the Ryu Myaku would change direction so they went to Senjo Gahara. Kenshin and Kaoru visit the graveyard and do what they have to do, suddenly it started to rain so they went to a hotel to spend the night.
When Kenshin arrives at Kyoto, Misao asks whether he would like to go to a cheap inn. Rurouni Kenshin is a former assassin who wanders the country side of Japan. As Kenshin and Kaoru are returning from a play, they see this and Kenshin intervenes. The girls go shopping and bump into a pick pocket, they beat him up and get back their money. The pick pocket went and got all his men but they were defeated, meanwhile Kenshin and Aoshi talk and drink tea, they decide to take a walk and they see the girls. Daigoro attacks but pulls his back and is unable to move.
Outside the Beni Aoi was waiting for her and kidnapped her. While he wanders he gives protection to those in aid to redeem himself of the lives he had taken while an assassin when he served in the Bakumatsu war. A man called Sojiro Seta contacts Kenshin and brings him to meet Shishio that asks Sojiro to duel Kenshin. Soon the black knights arrive and including the leader of Sanada Ninja's, Misanagi. The police department slowly rebuilt their stations and Kenshin saw Jinpu off. Kaoru decided to accept him as a student and tried to teach him to be strong.
Kenshin left and went to tell Daigoro's teacher Katsu that his daughter was staying at the dojo, as Kenshin leaves the men earlier is trying to attack Kenshin. Now the water clan has come back and is creating their formation. Kenshin allowed him to keep the name and he and the rest set sail to go back home. Fearing for the safety of his friends he decides to go to this assassin and defeat him to ensure his friends stay safe. When Kanryuu poisons the population to get the school, Kenshin and the street fighter Sanosuke Sagara join forces to attack their common enemy. They find the trio murdered by Shishio's men and Kenshin defeats them in the nearby village. He seeks out the talented blacksmith Shakku Arai to repair his sakabato and finds that he is dead.