Kenshin goes off fishing to bring some food on the table. At the river he meets an old man who tells him the legend of the fireflies. At the end it is revealed the old man was telling Kenshin the tragic story of his dead lover, who died waiting for him to return from his long quest to master the sword. He gives Kenshin the message that once in his life, every man meets a woman he will never forget. After hearing his story, Kenshin brings back an iris flower, which he does not give to Kaoru.
A foreign prince is attacked by bandits. As Kenshin and Kaoru are returning from a play, they see this and Kenshin intervenes. During the attack the prince was injured, so Kenshin and Kaoru take them back to the dojo. As it turns out, Prince Shin looks exactly like Yahiko, and so Yahiko is put in his place to attend a banquet. At the banquet the bandits attack yet again, but our favorite samurai is there to protect Yahiko, along with Sanosuke.
When he finds himself under attack by the Kenwadan, a gang of masked men, a politician, Mr Takamori, throws the key to his safe into an alleyway. Unexpectedly, the key is promptly picked up by a dog, who then escapes with it into a river, despite the gang's frantic pursuit. While praying at the shrine for better luck at dice, Sanosuke comes across the dog, now half-dead, and carries it back to the Kamiya dojo to be looked at by Megumi. Cue comic adventures as the dog, which Sanosuke names Notaro, promptly tears the Kenshin Group's lives apart, eating their food, stealing and burying their possessions, and generally making a nuisance of himself. But it doesn't take the Kenwadan Gang long to track Notaro down. Will Kenshin and the others be able to fend them off and find the key before the gang do?
It is Tanabata, July 7th. Tsubame-chan, Kaoru, and Tae-san are window shopping. Tae tells Kaoru what an engagement ring symbolizes. Kaoru starts daydreaming about Kenshin asking her to marry him, the wedding, the wedding night and we break to Kaoru passed out flat on her back in the middle of the street with Tae leaning over her. Tae decides that Kaoru is frustrated and needs her help to find happiness with Kenshin. Kenshin goes fishing and comes back with a catfish. Kaoru apparently hates catfish. Kenshin takes a bite of fish and bites into a ring. Tae talks him into giving the ring to Kaoru. Turns out the ring belonged to a guy who was going to propose to his girlfriend, wonder how much trouble the Kenshin-group goes through to pry the ring off of her finger. From jujutsu, to checking through her underwear, all the way to intoxicating her with beer. Can they get it off, in time to to stop the hopeless romantic from committing suicide?
The Kenshin-gumi receives a letter from Misao. She reports on a murder mystery in Kyoto and a dead body with strange carvings on the flesh. Aoshi is approached by a man seeking protection from a written death threat. Aoshi refuses, but Misao sees the letter and takes it to Okina. 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.
Amakusa Shougo appears at the place Cho is protecting. He defeats Cho and then kills the man he came to kill. Cho tells Kenshin that Amakusa is better than Kenshin. Okina finds out that the three men Amakusa has killed were responsible for persecuting Christians during the Edo dynasty.
In Shimabara, Yahiko almost gets run down by a carriage carrying the Ambassador of Holland, Elsten-dono. Kenshin and Elsten recognize each other, since Kenshin saved Elsten's life 10 years ago at the end of the Edo dynasty. The Kenshin-gumi go to the ambassador's residence for tea and crumpets. Magdaria and Shougo are traveling by carriage, then boat to Shimabara.
The round man has Kenshin down and surrounded by the dogs, but then he loses the whistle with which he controls them. Kenshin ends up saving himself and the round man from the dogs. The round man is confused, since Kaioh-sama told him that Kenshin is a demon and has to be killed, but Kenshin saved the round man's life. The round man chains Kenshin to a tree and goes for Magdaria to see what he should do with Kenshin.
Sano is unconscious and lying on the floor of a cave. When he wakes up, he finds himself looking into the face of Magdaria. She notices he is hurt and takes him back to her home in the hill. While she patches him up, they have an argument and she locks him in the room. Meanwhile, Kaioh, Santo, and Amakusa Shougo are plotting the demise of the Meiji government through the instigation of a civil war, but they are disagreeing over price and methodology. Carrying a gun, Magdaria returns to the room where she locked Sano, but he has disappeared.
Misao tells Kenshin what she knows, Shougo and Magdaria(Sayo) are hiding a secret, in the past Shougo was able to help cure people's illness because he had study under the field of medicine, but he can't cure his sister and she's dying. Soon after Kenshin, Kaoru, Yahiko and Kenshin leave and gets caught by someone. Later on, Magdaria is informed that Kaiou has her medallion so she went into his room and went looking for it. She found some more interesting things and found out that Kaiou is going to betray her and her brother. 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.
Kenshin is caught by someone and he takes him out quickily. Meanwhile the rocks had fallen and Shouzo was trapped, Sanosuke and Magdaria managed to get out fine. Sanosuke and Magdaria worked together and got him out. Shouzo got away and went to report this to Shougo. Meanwhile someone showed up to take Sanosuke out, it was no problem and he was defeated, but he would not give up, he attacked once more time but Misao and Yahiko helped. Together they got out of the cave but Magdaria was very sick and Sanosuke ran as fast as he could to bring her to Elsten. Later on, Shouzo had overheard Kaiou's plans and tried to fight him but was defeated, as a last resort he threw some pipe bombs that Sanosuke gave him and killed Kaiou.
The army started to prepare themselves to fight Shougo and kill everyone else. Sanosuke continued to try and bring Magdaria to Elsten. After achieving many obstacles Sanosuke finds some luck and sees Elsten. Elsten was interfering too much so Santo tried to kill him but Magdaria jumped in and was shot. Sanosuke beat up Santo and returned Magdaria's medallion back to her, shortly after she died. Elsten left and tried to hurry and get to the holy hill to stop the fight. Meanwhile Kenshin finally arrived and tried to stop the fight, he had found Shougo and would fight him if he would force the children to sacrifice themselves.
Misao was caught by two men and was brought to the leader of the army, she kept on telling them that Kenshin is negotiating with Shougo. Finally Elsten arrived and tried to stop the attack, he was only able to stop it for an hour, after the hour they would attack. Misao went off to tell Kenshin he has an hour and if he was successful she would throw a signal out to let him know. Kenshin had already started to fight Shougo, finally both used the succession technique and Shougo was defeated. Kenshin had gained his sight again and Misao just arrived.
The war was over and Shougo surrendered. Kenshin visited Elsten to find out what will happen to the believers and so on. Elsten is waiting for the government's decision and it should arrive shortly. 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. Meanwhile Sanosuke gives Kaoru a letter and she makes a visit to Shougo. Kaoru gives the letter to Shougo and leaves. Shougo makes a last visit to his sister's grave and left to go to Holland.
Kenshin and the rest are in the restaurant eating, suddenly a group called Tengu creates a disturbance, Yahiko and Misao take them outside and fight them. Then a man claiming to be the legendary Battousai arrives and scares them away. 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. Kenshin and the others help out and have a place to stay. The Tengu group is getting restless and wants to kill the Battousai, a man named Anzai arrives and says he will kill the Battousai. He arrives at the dojo and wants to fight the Battousai, Kenshin came right on time and defeated him. Kenshin allowed him to keep the name and he and the rest set sail to go back home.
Kenshin and the rest are walking through the forest, they end up going to a restaurant to eat, and when the time came to pay for it, Kenshin had lost Kaoru's money. Kenshin and the rest offered to work off the money. Kaoru and Misao were making trips to send people their meal and accidentally went into the wrong room. Later that night Misao and Kaoru were in the hot springs and they spotted someone. They realized it was an artist seeking inspiration and Kaoru was it. The artist had fallen in love with Kaoru but Kaoru was in love with Kenshin, Misao had an idea and told Sanosuke, Sanosuke told the artist if he can hit Kenshin he will hook him up with Kaoru. No matter how hard the artist tried he couldn't hit Kenshin. Finally he got his inspiration and drew a portrait of Kaoru and gave it her. Kenshin and the rest left and saw Kaoru's picture, it was an abstract drawing and they laughed while running away.
A man is talking about people being able to go to the moon, but the others laugh at him, he left with his teacher and forgot his books. Yahiko went to return the books but the man (Daigoro) and his teacher was going to be attacked. Yahiko and everyone helped out and were able to protect them, then Tetsuma appeared and scared them away. Daigoro's teacher than kicked him out of his dojo since he wasn't very good with a sword. Kaoru decided to accept him as a student and tried to teach him to be strong. A girl named Itsuko came and tried to bring him back but Daigoro refused and Itsuko stayed behind. 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.
A bunch of men are ready to attack Kenshin but Kenshin has no idea who these people are, they tell Kenshin that they are the Beni Aoi, Kenshin still doesn't know who they are, the leader figures out Kenshin wasn't hired as a bodyguard and left. Daigoro continues to train and has a match with Yahiko. Daigoro attacks but pulls his back and is unable to move. Itsuko is cooking and Kaoru shows up, she teachers her to cook but forgot to buy something so she left. Outside the Beni Aoi was waiting for her and kidnapped her. 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.
Itsuko was kidnapped and Katsu had received a letter about it, Kenshin paid a visit to him and found out that Katsu was hiding someone's money and the Beni Aoi wanted it. Katsu was suppose to arrive at 2:00am at a temple, and if he cooperates his daughter would not be harmed. Kenshin was told not to come but he still went as well as everyone else including Daigoro. They arrived at the temple first and Daigoro say Itsuko, she tried to run for it but tripped, Daigoro charged forward and was stabbed.
Daigoro was just stabbed and Kenshin stepped forward to fight the leader while the others took care of the rest. The leader was defeated and shortly the police arrived and arrested the Beni Aoi. Back at Katsu's home, Tetsuma was caught, Katsu knew it was him looking for the map to the hidden money. Tetsuma try to reason why Katsu but it wasn't enough then he tried to fight him but Kenshin stepped in. Kenshin defeated Tetsuma and he then knew what he did was wrong and turned himself in.
Yutaro returns back to the dojo with Professor Hans. Yahiko sees Yutaro and they have a friendly fight. Meanwhile the Black Knights are after professor Hans and want something from him. Since Yutaro is back Kenshin and everyone go to a restaurant and eat to celebrate Yutaro's return. The meal was finished and Professor Hans and Yutaro left, as Kenshin was leaving he noticed someone so he stayed behind. Professor Hans was attacked and a map was taken from him, he was badly injured and Yutaro couldn't do anything, Kenshin stepped in and fought one of the men but they retreated since they heard people calling Kenshin. Professor Hans was brought back to be treated and he told Yutaro that there's a map under the dojo and he must protect the divine medicine. Meanwhile the Black Knights had the map and were celebrating someone caused a ruckus and revealed them self.
The Sanada Ninjas have joined the Black Knights in the search for the Divine Medicine but the Sanada Ninjas will take over Japan. Meanwhile Yutaro has Professor Hans note book and reads it, he soon finds out that there is a medicine that can possibly cure any illness. The Black Knights are elites in their field and can be dangerous, they are after the Divine Medicine so they can sell it and gain money and start to rule the world. Kenshin figures out that the Divine Medicine is somewhere in Suwa Sea so they take a trip there, trying to find any hints Kenshin asks local people questions. As they are moving, Sanada Ninjas attack Kenshin and the others, the Oniwabanshu helped and stopped the attack. The ninjas retreated and went back to base, the head leader of that group was getting annoyed of the outsiders and was arguing with the leader of the ninjas, the Black Knights step in and fight that particular group. Later on, Misao tags along with Kenshin and they get ready to get into Sanada's base.
Kenshin and the rest continue to use their hints and search for the divine medicine, suddenly Yahiko is unable to walk anymore, he had a fever. 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. After using all the hints Kenshin and the others were able to get into a cave and was on track, finally near the end, the path way was open. Soon the black knights arrive and including the leader of Sanada Ninja's, Misanagi. One thing that Yutaro was unable to read was the last paragraph and the floor collapsed and they fell into the ground.
Kenshin and the rest fell underground and had no idea of what to do. Meanwhile Misanagi and the Black Knights enter the path way and begin to move toward the divine medicine. Later on, gas was leaking in and in less than half an hour Kenshin and the others would be goners. Sanosuke punched the wall and water came rushing out, because of that they were able to escape. Outside Yutaro found someone, it was a ninja named Kaita. He was injured and was going to die if not treated. Yutaro worked hard and treated Kaita's wounds, he woke up and helped them by using a shortcut so they could get caught up. Finally getting inside there were three guards, Zan, Ren and Baku, they attacked everyone and Ren was able to cancel out one of Kenshin's attack.
Kenshin and Sanosuke continue to fight Zan and Ren while Baku is unnoticed. Sanosuke is having a bit of trouble but with the help of Kaoru, Sanosuke is able to defeat Zan. Kenshin's senses are being distorted and is having trouble with Ren, Kaita told Kenshin to attack the bats, after that everything was more clear, Ren and Baku were defeated shortly. A bat slowly flew away and tried to report back, Kenshin and the others followed it and found the divine medicine. Lieutenant Melder had betrayed Misanagi and Schneider would not put up with it so he fought Melder but got injured. Kenshin arrived and was going to fight Lieutenant Melder.
Lieutenant Melder charges forward and attacks Kenshin, it would seem that Kenshin has a disadvantage and was injured badly, Melder continues to attack but creates a spark and ignites a flame with the oil on the ground, the divine medicine started to burn fast and Renz went to get a sample but Yahiko and Yutaro tried to stop him. Kenshin uses his succession technique and defeats Melder but was badly injured, Kaoru helped carry Kenshin to safety. Kaita helped defeated Renz and brought him to safety, Yutaro ran into the flames and grabbed a sample of the divine medicine, Sanosuke ran in and grabbed Yutaro out. The divine medicine was burned down and everyone got out except for Melder, Professor Hans recovered thanks to the medicine and received a report saying that the Black Knights have handed themselves over and the remaining Black Knights will be looked closely. Later on, Professor Hans and Yutaro are about to leave and Kenshin and the rest see them off.
A day in the dojo where Yahiko is training, Yahiko is training with Misao and she's deciding it's about time she leaves. Omasu, Ochika and Aoshi arrive and are ready to take Misao back to Kyoto. Misao changes her mind and decides she doesn't want to go back, and then the females decide to go shopping. The females leave and Sanosuke and Yahiko are up to something, they believe that they are going to go and eat something without them so they tag along. 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.
Two competing clans of Feng Shui users create a powerful magic around the land that Tokyo sits in circa 1604. After 275 years, this magic begins to reactivate and cause disasters in Tokyo. After each of these incidents, a man claiming to be a Feng Shui master appears to provide advice to the victims. However, as soon as the man leaves a mysterious entrepreneur turns up to offer his services, such as warding stones inscribed with the power of Feng Shui. 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.
The Fusui Master Jinpu had just saved Kenshin, they return back to the dojo and he explains everything. 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. Now the water clan has come back and is creating their formation. 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.
Kaoru was injured and the only way to cure her is to go into the mountains and find the dragon fountain and get the water only then she will be cured. Jinpu creates a plan, he and Kenshin will go and get the water, Sanosuke and his friend will find some sort of statue and will destroy it and Yahiko will stay behind to protect Kaoru. So far everything has been successful Sanosuke is doing fine, and Kenshin and Jinpu are on their way. Meanwhile the water clan is slowly destroying the Eigou formation, Kenshin and Jinpu finally make it into the mountain and Kenshin grabs the water, the caves started to cave in and Kenshin and Jinpu got out. The Ryu Myaku started to move east of Musashino and the battle was not over yet.
Kaoru was given the water and she started to recover, Kenshin and Jinpu left to Nikko to beat the Ryu Myaku before it was too late. Sanosuke and his friend went looking around for clues, finally they got possession of a book that gave many useful clues. It was hard to understand so Sanosuke and his friend went to find the author and he explained everything. Kenshin and Jinpu got to Nikko and the crest was gone, clues and hints were being pieced together and the water clan's plans started to become clearer. Sanosuke found Kenshin and Jinpu and explained everything, the Ryu Myaku would change direction so they went to Senjo Gahara.
Kenshin, Sanosuke and Jinpu went to Senjo Gahara and found the water clan, Jinpu went and attacked Reisui, and Reisui used his formation and proved to be more powerful than Jinpu. Meanwhile the author arrived and told the police and Sanosuke's friend to put the dragon statue in the center it will stop the Ryu Myaku. The Ryu Myaku had arrived and it was destroying the place, it hit the dragon statue but it was only weakened, Jinpu was able to stop it and the water clan was defeated as well as the Ryu Myaku. The police department slowly rebuilt their stations and Kenshin saw Jinpu off.
It's peaceful times and everyone is carrying about their life, Kaoru and Kenshin leave to visit a graveyard, Yahiko is helping at the Akabeko and Sanosuke is helping Megumi so she can make something for him to eat. 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. Meanwhile Sanosuke took a long bath and Megumi washed his clothes and he was forced to wear something else, soon everyone went to sleep. Kaoru had dreams of Kenshin wandering off again, she awoke and it was morning, Kenshin wasn't there, she found him at the beach and they talked for awhile. They got on to the boat and set sail to return back home. The boat arrived back in Tokyo and everyone was waiting for Kenshin and Kaoru to get back.