On December 10, 1867, Ryōma Sakamoto, a samurai destined to change Japan, was assassinated. It was revealed that he was a doppelganger, as he was killed by Ryōma himself, going under the name Hajime Saitō.
Saitō explained the events that led to that day. Just a few years prior to Ryōma's assassination, Japan had been ruled by the Tokugawa bakufu, also known as the Edo shōgunate, for 300 years. Their reign started ending when the black ships of the Western civilizations came to Japan and the bakufu didn't have the means necessary to defeat their advanced weapons. The samurai couldn't sit idly when their leaders appeared weak, so this led to a civil war.
On May 4, 1862, Ryōma returned by boat from Edo to Tosa for the first time in about a year. He saw a mother who had a daughter who was ill. She was told by a doctor that she had appendicitis and only a doctor who utilized Western medicine could treat it. The doctor intended to get the girl help, but the samurai of a high social class, the joshi, appeared at that moment. Japan at that time had a strict social hierarchy and people of a lower class were expected to stop and bow as the Joshi came by. The mother tried to rush by them, but she was stopped by the joshi. She tried to tell them that her daughter needed a doctor, but the joshi refused to let her by. Ryōma, a samurai of a lower class, the goshi, stepped in and told her to get her daughter to a doctor as he fought the joshi.
Ryōma was jailed in Kochi castle and was rescued, by Tōyō Yoshida, from execution at the hands of a Shirafuda Goshi, a samurai of a social class between the Goshi and the joshi. Tōyō was a high-ranking member of the Tosa government and Ryōma's foster father. Tōyō tells Ryōma to head to Kengoshi Academy, which is the secret training grounds of the Tosa Loyalist Party. Ryōma reunites with Hanpeita Takechi, who saved Ryōma from the fire that killed his family 15 years prior. Takechi announces to his men that Ryōma is second in command of the Tosa Loyalist Party, which doesn't sit well with the other members. Ryōma fights several men led by a samurai named Izō Okada and proves that he is worthy of the title.
The next night, Tōyō is at the castle with 500 Tosa Loyalist Party men to force the old governors out and enact change in Tosa. As they are about to put their plan into motion, a masked man enters and kills Tōyō with a style of martial art that neither Ryōma nor Takechi had seen before. Takechi chases after the man, and Tōyō, with his dying breath, tells Ryōma that the future of Tosa is in his hands. However, the castle guards blame Ryōma for the murder of Tōyō, and Ryōma has to fight his way out of the castle. Ryōma tells
Ryōma tells Takechi to stay out of sight, or he'll be accused of murder as well. He then dives off a cliff, fleeing the guards, and vowing to track down the man who murdered Tōyō.
The Tosa loyalists believe the emperor of Japan should rule Japan and are determined to bring an end to the rulers of Japan, the Tokugawa bakufu, by any means necessary. Many loyalists gather in Kyo, which is home to the seat of the emperor.
One year after TōyōYoshida was killed, Ryōma Sakamoto rented a room in Kyo. In an effort to avoid execution due to the fact that the Tokugawa bakufu believe he killed Tōyō, Ryōma used the alias Hajime Saitō.
Oryo is a woman who works as a maid for Otose. The latter is the landlady of Teradaya, a large bed-and-breakfast-style inn where Saitō was staying.
Saitō has spent the last year talking to people in dojos to see if he can find information about the masked man who killed Tōyō. He explains the masked man's technique as an obscure martial art from the countrywide that has elements of jujutsu, staff technique, and old martial arts that put an emphasis on function over form. He managed to learn that the style of martial arts used by the masked man was called Tennen Rishin and was taught in the Shieikan dojo in Edo. However, he had trouble finding out more.
An information dealer named Ginji the Crow was paid by Saitō to find more information about the masked man and his technique. Crow was coming up empty in regards to his assigned task so he approached Saitō in a dojo that had uncooperating students that were more interested in fighting Saitō than helping him. Crow wants to know if Saitō is sure that the mysterious masked man is in town. Saitō tells Crow that the Shieikan dojo in Edo closed and its members moved to Kyo. After being assured that the mystery swordsman is in Kyo, Crow vows to redouble his efforts.
Saitō is told by a mysterious man calling himself Matsusuke Niibori to find an information broker named the Bathkeeper of Sai. Saitō discovers that the people from the Shieikan dojo joined the special army for the bakufu, the Shinsengumi.
In the middle of their conversation, a man named Kichinosuke Saigō demands to get information from the information broker. Saitō fights Saigō and when the former wins the latter takes him out drinking. Saitō learns that Saigō is the General Commander of the Satsuma Domain's army.
Upon leaving the bathhouse, Saitō is approached by a mysterious man in a hat who tells him to meet at the slum district, Mukurogai. At Mukurogai, which he reached by boat, Saitō learns that the man is Izō Okada. The two fight and Saitō wins. Okada reveals that Hanpeita Takechi, the man Saitō considers a brother, is waiting for him deep in Mukurogai.
Hanpeita Takechi reveals that he still works for the bakufu and is now a joshi. He feels that Saitō is wasting his time by trying to get revenge on Tōyō Yoshida. Takechi feels Saitō should be looking at the bigger picture to get the emperor back in power. Saitō, disgusted that Takechi is working for the people who killed Tōyō, tells him that he is joining the Shinsengumi to get revenge for his foster father and says that he will never move on until he does.
The following day, Saitō goes to the Shinsengumi barracks to infiltrate their ranks. After Saitō defeats Second Division Captain Shinpachi Nagakura, he is made a member of the Shinsengumi. However, he is challenged by First Division Captain Soji Okita. When the fight between the two is a draw, Deputy Chief Toshizo Hijikata takes Saitō inside.
The deputy chief orders Third Division Captain Keisuke Yamanami to fight Saitō to the death. Saitō wins, but when he refuses to take his life, Hijikata does instead. After stating that Yamanami tried to desert the Shinsengumi and warning that no one who ever leaves remains alive, Hijikata tells Saitō he will be the new third-division captain.
The next day, Saitō is made the third-division captain, upsetting several other captains because Saitō is a new recruit. The captains who are upset are Seventh Division Captain Sanjuro Tani, Tenth Division Captain Sanosuke Harada, and Fourth Division Captain Chuji Matsubara. Ito Kashitaro, the military advisor, then accuses Hijikata of taking the power of the Shinsengumi for himself during Chief Isami Kondō's long absence.
The meeting soon concludes, and Eighth Division Captain Heisuke Tōdō gives Saitō a bag with a blue haori, which is a piece of clothing that all Shinsengumi captains wear.
On the way back to the inn, a priest and a young girl are trying to keep a house from being foreclosed. Saitō volunteers to take over care of the house and to grow and harvest plants that would be sold at the market or cooked into meals. The girl, who is named Haruka, would maintain the property.
At the inn, Oryo gets angry that Saitō became a Shinsengumi and runs away. Otose tells Saitō that her parents were murdered by members of the Shinsengumi. Saitō goes after Oryo, and when he finds her he explains that he will change it from within by making sure people under his command don't indiscriminately kill people.
Saitō meets with a mysterious samurai named Nakaoka Shintarō from Tosa. Shintarō knows that Saitō is really Ryōma Sakamoto and explains that he was a Tosa samurai who was present when Tōyō Yoshida was murdered. Ryōma is the prime suspect, but Shintarō suspects that Hanpeita Takechi was the murderer. Saitō tells Shintarō about the masked man and the two acknowledge they are both working towards the same goal of finding Tōyō's real killer.
Saitō heads to the Shinsengumi barracks for his first day and is shown around the grounds by Heisuke Tōdō. Saitō learns that he has to control a unit under his command to fight against combatants to protect the people of Kyo, as well as to take care of anyone who defects from the Shinsengumi.
On his way back to the inn, Saitō is stopped by Susumu Yamazaki, an inspector for the Shinsengumi who is posing as a homeless man. He tells Saitō the location of Akimoto, a defector from the third division, so Saitō heads over to get him before he leaves the area.
When he arrives, Tōdō is there to make sure Saitō does his job as well as to stand guard to make sure Akimoto can't escape. Once inside, Saitō meets a woman named Mizuki, who lets him know Akimoto is using the outhouse. When Akimoto is finished, he gets jealous that Saitō is talking to Mizuki.
The two men fight, and when Saitō wins, he decides to let Akimoto leave, telling him to go out the back because Tōdō is guarding the front. As Akimoto tries to get Mizuki to go with him, Tōdō kills him with his sword. He tells Saitō that he has to lose his conscience because, by the code of the Shinsengumi, all defectors must be killed.
Saitō goes on a raid at a gambling den. However, before he reaches his destination, he meets up with the informant Crow. Chuji Matsubara, the fourth division captain sees them talking and immediately kills the informant.
At the den, the seventh division captain, Sanjuro Tani runs in alone and is slain by Okada Izo. The ninth-division captain, Mikisaburo Suzuki, is slain next. Genzaburo Inoue plans to take him down with Saitō, but the latter takes him on alone due to Inoue's advanced age.
Saitō defeats Izo, and when given the chance to kill him declines to do so. The officials come in shortly afterward to bring Izo in, where he will likely be tortured and killed. Inoue revealed that he called the officials and that he was testing whether Saitō would kill Izo after defeating him.
Susumu Yamazaki tortured a loyalist named Furutaka Shuntaro to get him to talk. He reveals that forty loyalists planned to set fire to the palace and kidnap the Emporer. He mentioned the name Nakaoka so Saitō goes to the inn to talk to Nakaoka Shintarō.
Saitō reveals his worry over possibly sending Izo to his death, but Nakaoka assures him that he is smart and strong enough to come up with a way to escape. Nakaoka then reveals that he is not the Nakaoka they mentioned but said that he would get in contact with the loyalists to let them know the Shinsengumi planned to attack.
The captains combine their teams and then split up, with the two teams going to different inns. Saitō goes with the team to the inn in Rakugai while the others go to the inn in Fushimi.
No one is at the inn, but the Shinsengumi receives word that the Choshu are at Ikedaya. Once there Nakaoka covertly lets Saitō know that he wasn't able to get the loyalists out in time. So, Saitō has to fight through the Choshu fighters until he reaches the leader of the Choshu Domain. It is Matsusuke Niibori, but he reveals he is actually Kogoru Katsura. Apprehending him was the reason why the Shinsengumi was at Ikedaya.
Katsura reveals that he knows Saitō is really Ryōma Sakamoto, tells him that they are on the same side, and points him toward Isami Kondō. He is the Shinsengumi chief, and as such is someone that may be the masked killer. He convinces Saitō to throw the fight, which allows Katsura to escape. However, Nagakura notices Saitō doing so.
As it was clear the Choshu shishi were aware of the raid, it was apparent that there was a traitor in the Shinsengumi. Deputy Chief Hijikata reveals that Chuji Matsubara, the captain of the fourth division of the Shinsengumi, is the traitor. Saitō is given the task of slaying him, but Matsubara tries to shift the blame to Saitō by saying that he joined under false pretenses. Before he can continue further, Genzaburo Inoue slays Matsubara himself.
Afterward, Shinpachi Nagakura reveals that he is aware that Saitō let Katsura get away. He lets the incident go as he doesn't want any more Shinsengumi captains to die. However, he warns Saitō not to do something like that again.
At the Satsuma army barracks, the admiral of the navy of the bakufu, Rintaro Katsu, introduces Kichinosuke Saigō to a man claiming to be Ryōma Sakamoto. The imposter Ryōma acts as a mediary between the Japanese and the British, providing the bakufu with British weaponry. He wants to do the same with the Satsuma army.
Saitō asks around the Shinsengumi barracks to see if he can talk to Kondō. After getting nowhere talking to the deputy chief and other captains, he gets word that Kondō is at Asahi. Saitō fights Kondō, who claims he is the man who killed Tōyō Yoshida. However, when Saitō defeats him, he realizes he is not skilled enough to be the killer.
Kondō reveals that he knows Saitō is Ryōma Sakamoto, and tries to convince him to join a movement that intends to burn down Kyo and rebuild the capital in Edo. If Saitō joined the movement, Kondō would tell him the identity of the masked killer. When he refuses, stating he is going to continue investigating on his own, Kondō allows Saitō to stay in the Shinsengumi even though the imposter Ryōma is the man they are hunting down. When Saitō leaves, Genzaburo Inoue reveals that he knows Saitō's real identity as well.
With his identity known by the chief and his true purpose to enter the Shinsengumi to look for people who use the Tennen Rishin style of martial arts known by the captains, Ryōma meets up with Nakaoka. He reveals his predicament and they are both aware that Saitō can find himself in danger with the Shinsengumi at any time.
For the moment, Saitō decides to treat it as business as usual and goes to the Shinsengumi barracks. He is told that Soji Okita wants to see him. Okita tells Saitō that he wants him to be a part of a raid on the Sengoku residence. Okita believes that loyalist shishi are being harbored inside, but Saitō is wary of the plan because even the chief doesn't know about it. Okita tells Saitō that he only wants him and the division he commands to join. As Saitō is only interested in finding Tennen Rishin martial artists, Okita believes he will be able to get the glory all to himself. Reluctantly, Saitō joins Okita on the raid.
After fighting through the loyalists, Saitō reaches Sengoku. However, Sengoku and Okita reveal it was a setup as Sengoku knowingly put the loyalists in his mansion up for slaughter to become part of the Shinsengumi. However, after Sengoku revealed the plan, Okita kills Sengoku for talking too much.
Okita tells Saitō that he knows he is Ryōma Sakamoto and says that he was the masked killer. The two fight and Ryōma wins. However, he realizes that Okita was not the killer as his fighting style is too much like a mad animal whereas the killer had moves that were precise and technical.
Okita reveals that he was present when Kondō revealed Saitō was Ryōma and says that he lied about being the killer so that he could get the chance to fight the real Ryōma, without holding back.
When the two leave the Shinsengumi barracks, Oryo arrives with an urgent letter from Nakaoka. The letter states that Hanpeita Takechi, the man Ryōma considers his brother, has been executed. Ryōma goes back to the inn where Nakaoka reveals that Izō Okada confessed that Takechi was behind the loyalist attacks. As a result, Takechi was sentenced to death by Okada.
Distraught with the news, knowing that he was the one who got Okada taken into custody, Ryōma took off his Shinsengumi haori and began drinking heavily. Oryo tried to get Ryōma to stop drinking, but he left the inn to drink more. After drinking in Fushimi, Ryōma was approached by a mysterious woman who invited him to a bar named Matsunoi. Upon arriving, it is revealed that she is Ikumatsu, Kogoru Katsura's lover.
Katsura tries to get Ryōma to join the Choshu Domain, but the latter states he is not interested. Upon leaving, the two witness Kichinosuke Saigō of the Satsuma Domain save a dog from being hit with rocks by punks. Katsura and Saigō begin fighting each other with their swords, but Ryōma takes their swords away and says that he is not interested in witnessing a turf battle between the Choshu and the Satsuma. He instead tells them to fight each other, as well as himself, with their fists.
After winning Ryōma says that he gets to choose their punishment and makes them go drinking with him. They all get extremely drunk, but Ryōma doesn't feel he is inebriated enough, so he takes them all to Gion. They all get even drunker and Katsura reveals that Saito is actually Ryōma, making Saigō aware that the Ryōma Sakamoto he met was an imposter. The latter, right before passing out, tells Katsura and Saigō to stop fighting with each other.
Ryōma wakes up at the inn, and Oryo reveals that Katsura and Saigō dropped him off there. She also says that the two had agreed to stop fighting and left in good spirits. Ryōma is still distraught by the news of his brother's execution and asks Oryo to stay with him through the night.
When Oryo wakes up in the morning, Ryōma is not in his futon. She goes outside of the inn looking for him, only to see him dressed in his Shinsengumi haori. Ryōma has once again taken up the identity of Hajime Saitō and he tells Oryo that he still has work to do. Afterward, Shinsengumi inspector Susumu Yamazaki discretely leaves Oryo a message, revealing that the two have a connection.
Arriving at the Shinsengumi barracks, Saitō learns that Genzaburo Inoue has been murdered and his body was found floating in the river. Sanosuke Harada is furious that another Shinsengumi captain has been killed as he heard the loyalists call the Shinsengumi pawns. He wants to go out and murder all of the loyalists to make civilians fear the Shinsengumi again. However, he is stopped by Okita Soji, who says that he will go on a murderous rampage himself and tells Harada that he is not a pawn of the bakufu, but rather a pawn of the Shinsengumi. Angered, Harada leaves the barracks to do his plan himself.
Deputy Chief Toshizo Hijikata tells Heisuke Tōdō to go after Harada and get him drunk because since he has no loyalty to Inoue, that will make him calm down and he will sleep off his anger. He tells Saitō to go after Okita, warning him that it will be harder to get him to stop seeking vengeance because Okita and Inoue had a history together.
After defeating some of the first division fighters harassing civilians, Saitō goes to the harbor where Inoue's body was discovered, knowing that Okita would head there first.
Upon arriving, the informant tells Saitō that Ito says to do everything in his power to stop Okita. He also tells Saito to go to Mukurabi because Okita is searching for a komuso, a monk who wears a basket on his head called a tengei that is meant to symbolize the absence of ego.
After defeating more fighters from the first division, Saitō arrives at Mukurabi, where he is told Okita is waiting for him. Okita wants to kill Saitō because everyone says that the man who killed Inoue was Ryōma Sakamoto. Okita believes it is not the imposter Ryōma. Saitō had a motive because Inoue was the masked fighter who killed the real Ryōma Sakamoto's foster father.
After defeating Okita, he reveals that his master was Inoue, who he calls Gen-san, and that he really did kill Tōyō Yoshida. He reveals that Inoue was not his real name, only for Isami Kondō to arrive and tell Saitō that he would reveal the truth.
The Shinsengumi was originally known as the Miburoshigumi. The Miburoshigumi was formed by the members from the Shieikan dojo, including Hijikata, Yamanami, Okita, Nagakura, Todo, and Kondō, with support from the bakufu to protect the Shōgun in the capital. It also included three founders from the Mito Domain, Kamo Serizawa, Goro Hirayama, and Jusuke Hirama.
The previous year, Chief Kamo arrived back at the Miburoshigumi barracks from a secret mission from the Mito Domain to kill Tōyō Yoshida in Tosa. He had been ordered to do so by the Mito Domain, who said their dappan would only be forgiven if the job was completed.
However, upon his arrival, he was confronted by Okita, Inoue, and Nagakura. They have been following the Mito faction because they felt Kondō was too lenient in letting them join the Miburoshigumi despite being criminals. Okita said he was tired of the Shieikan faction being pushed aside in favor of the Mito faction.
They drugged Goro and Jusuke so that they would only have to fight Kamo. After killing Kamo, they planned to slay the other two as they slept. After Kamo killed Inoue and Nagakura, Okita sliced Kamo's face, leaving a scar. Goro and Jusuke woke up just as Okita was about to slay Kamo. The two protected their captain, killing Okita.
Kondō and Hijikata arrived soon afterward. Kondō was impressed that Kamo, a master of the Mito Tengu style of martial arts, was able to defeat them.
Despite not initiating the fight, Kamo was prepared to commit seppuku if Goro and Jusuke's lives were spared. The two refused to have their comrade take his life for theirs, so they spoke up letting them know that they killed Okita to save Kamo.
Kondō determined they acted in self-defense, but felt he had to do something because the death of Okita, the man known as the wolf of the Miburoshigumi, would make them look weak to the public, causing them to be disbanded due to the loss of support from the bakufu.
However, Kondō revealed that he had fooled the bakufu as he really formed the Miburoshigumi to change Japan. To do that, he needs all of the strength he can get. Thus, Kamo took the identity of Inoue, Goro took the identity of Okita, and Jusuke took the identity of Nagakura.
After that night, the name of the Miburoshigumi was changed to the Shinsengumi. They leaked a rumor that Kamo had been executed for murdering Tōyō and the Shinsengumi captains started dressing in blue haori. To make sure the secret never left the group, the captains determined that deserters would have to be slain.
The day after Kamo became Inoue, Kondō had him train all of the captains from the Shieikan in the Mito Tengu style. It was renamed the Tennen Rishin style, and the captains intended to spread it across Kyo and then to the rest of the world. The idea was to continually recruit the strongest swordsmen, which is why they allowed Ryōma to join.
Kondō then reveals that the man who ordered the assassination of Tōyō was the imposter Sakamoto Ryōma, the komuso who also assassinated Kamo. He tells Ryōma and Goro that the inspector, Susumu Yamazaki, revealed that the imposter has been staying at Teradaya, the same inn where the real Sakamoto Ryōma has been staying. Ryōma decides to remain as Captain Saitō until he can find the imposter and learn the truth about his foster father's death.
Upon arriving at Teradaya, Ito and Takeda are there with the men from their divisions. Okita tells Ito that Kondō wants to see him over retirement, and Ito leaves with Takeda and the men from both of their divisions due to Ito's desire to become captain himself.
Saitō wants to save Oryo and Otose from harm, so they head to the back to sneak in. However, once he finds and tells Oryo that the Shinsengumi are there for Sakamoto Ryōma, she yells to warn him that the Shinsengumi are there for him.
Saitō and Okita fight their way through the inn, but when Okita slices the imposter's back, Ryōma is stunned because he has the same scar as that of Hanpeita Takechi, the man he considers his brother. This hesitation allows Hanpeita to escape and for Commander Tadasaburô Sasaki of the Mimawarigumi, the police force of the bakufu, to arrive and take over.
The Mimawarigumi were ordered to take over the capture of Ryōma Sakamoto from the Shinsengumi by the Minister of the Tokugawa Bakufu Navy, Katsu Rintaro.
Saitō heads back to the inn to discover the reason why Oryo warned the fake Ryōma Sakamoto, Hanpeita Takechi. She tells her that a man named Ryōma Sakamoto was a loyalist shishi who paid his respects after her father died. He made a deal with her to work for the loyalists in exchange for payment that she could use to support her mother.
He gave Oryo money to take the job at Teradaya to keep an eye on Hajime Saitō. When she gave her the job as a maid, Otose tells Saitō that she was left payment as well. After they revealed the truth, Saitō tells Oryo and Otose that he has been using a fake name and that his real name is Ryōma Sakamoto. Oryo then tells Ryōma that the inspector, Susumu Yamazaki, also knows the imposter Ryōma.
Back at the barracks, Ito is furious that Okita lied about Kondo retiring. He, Takeda, and Heisuke dislike the orders Kondo has been giving lately and think it is time for the Shinsengumi to get a new chief.
Ryōma talks to Kondō, who reveals that the Satsuma and Choshu united to become the Satchō Alliance to try to take down the bakufu themselves. Saitō was the person who made this happen, but he doesn't remember doing so because he was nearly passed out drunk at the time.
Kondō wants to end the Imperial Court before Japan becomes into the midst of a Civil War. Saito doesn't want him to do so as burning down the country would lead to innocent people, including women and children, being killed.
However, Kondō doesn't see any other way to stop the Satchō Alliance because he doesn't want the country to become a battlefield for foreign powers. Saito suggests stopping the bakufu rather than the Alliance. If the bakufu surrendered to the Satchō Alliance, there would not be any reason for a war.
Kondō suggests getting the Tokugawa bakufu to listen by getting the Edo Shōgun to return the government to the Emperor, restoring the throne in a Great Restoration. They intend to do this by going to the Shōgun in person and talking him into surrendering.
Ryōma wants to talk to the inspector before heading to Edo to infiltrate the castle and talk to the Shōgun, but Kondō tells him that Yamazaki was found murdered inside the Shinsengumi barracks.
Knowing that his only source of information about his imposter was dead, Ryōma goes to sleep at Teradaya. In the morning, Ryōma and Goro once again take on the identities of Saitō and Okita and take a message from Kondō to the Shōgun on a ship heading to Edo.
The message is too exquisitely calligraphed for Okita and Saitō to read, so a warrior reads it to them. The message calls for the end of the bakufu and the restoration of the Emporer and the Imperial Council. Okita suggests that they add something to it, so Saitō has the warrior add that the caste system be abolished and that all positions, including those of the council, be assigned by skill rather than class.
Once in Edo, Saitō walks up to the gates of the palace and demands to see the Shōgun. The guards refuse and draw their weapons, but before they can fight, Okita uses a cannon to blow a hole right through the gates.
Okita and Saitō fight their way through the palace until they are separated. Saitō defeats the Shōgun and tells him he is not there to kill him because another Shōgun will be installed in his place. He tells the Shogun that a war between the bakufu and the Satchō Alliance would destroy Japan, and tells him there is another way. Saitō hands the Shōgun the message and tells him to consider it.
While Okita and Saitō are taking a ship back to Kyo, the bakufu agreed to the terms in the letter. This angered Hanpeita Takechi, posing as Ryōma Sakamoto, so he made new plans.
When Okita and Saitō arrive in Kyo, they discover that the city has been lit on fire. After going to Teradaya to find out that Oryo and Otose already fled the city, they go to Gion to confront Kondō. However, on the way they have to fight through Commander Tadasaburô Sasaki of the Mimawarigumi, who blames the Shinsengumi for the blaze.
Saitō witnesses Harada Sanosuke setting the city on fire and telling his men to loot the burning buildings. After defeating him, Saitô ignores his pleas for help as Harada is killed after a building that he had lit on fire collapses on top of him.
Upon reaching Gion, Saitō finds Kondō dying on the floor. Kondō tells Saitō that the imposter Ryōma is going to kill the emperor and gives him a note with his final plan.
At the palace, Izō Okada is waiting for Saitō and the latter hopes that the former is really the imposter. Izō tells Saitō that he killed Kondō and that he has been waiting to fight the real Ryōma and that he will tell him the truth after he is defeated.
After the fight, Izō is dying as he tells Ryōma that he is jealous of him because Hanpeita considered him a brother when all Izō wanted was for Hanpeita to see him that way. Izō tells Ryōma that Hanpeita is really the imposter and that he is in Kyo.
The next morning, Kyo is smoldering after the fire has been put out. Ryōma leaves his haori at the gates of the Shinsengumi along with Kondo's note, but he is confronted by Toshizo Hijikata, Soji Okita, and Shinpachi Nagakura. Hijikata tells Ryōma that Soji told them his real name. Okita tells Ryōma that he is going to need backup and Hijikata gives him his haori back saying Saitō still has unfinished business.
Hijikata calls a Shinsengumi meeting and he, Okita, Nagakura, and Saitō are waiting for Ito, Takeda, and Heisuke to arrive. Hijikata tells them the magistrate's office investigated and determined that the Shinsengumi was responsible but that they were able to settle things by claiming that the tenth division captain, Sanosuke Harada acted alone.
Hijikata tells them that they are aware Kondō didn't give the order and they know the people responsible are Ito, Harada's tenth division, and Takeda's fifth division. If Kondō had really set fire to Kyo he would have given the signal to disband the Shinsengumi. Because he knew the order didn't come from the chief, Hijikata had the Shinsengumi work quickly to put the fire out.
Hijikata surprises those not in the know by announcing that Hajime Saitō would be the next captain of the Shinsengumi. Ito tries to stop this by saying the captain should have culture, knowledge, and morals, claiming that he has all of those qualities. He trips up when he said that he would carry on the legacy of their fallen captain even though no one said that he was killed.
Hijikata, Okita, Nagakura, and Saitō all draw their swords intending to slay Ito but Heisuke Tōdō fires a gun to get them to stop. Ito laughs as Takeda rises from his sitting position, letting everyone know he was in on the plot to murder Kondō as well.
Ito reveals that he convinced many of the men in the lower Shinsengumi ranks to support him as captain. The three mutinying captains take off their haori and Ito announces that they are leaving to form a new organization known as the Goryo Eji.
Hijikata reveals that the meeting was the plan Kondō left, in his letter, so that he could flush out the traitors. Heisuke Tōdō comes into the room revealing him to be a double agent.
The imposter's plans were in jeopardy due to the Great Restoration. Because of this, he planned to move forward quickly with his plans to use the Satcho Alliance to fight the bafuku since he knows the former wanted to create a new government. When the two were at their weakest, the Tosa loyalist party would wipe them both out.
Saitō wants to use the meeting to get the imposter out in the open but in order to do so he has to let Kogoru Katsura of the Choshu Domain and Kichinosuke Saigō of the Satsuma Domain in on the plan. He can't do it himself, and neither can any of the other chiefs, because the Goryo Eji is all over Kyo and all of their faces are known by them.
At that moment, Nakaoka revealed that he is back from an information-gathering trip to Tosa. He heard most of their conversation and states that he, Oryo, and Otose, will handle things. Otose reveals that she has a new inn that has just been built that she calls Omiya. Because of the attack on the Teradaya by the Shinsengumi when they were there for the imposter, Otose had a new inn constructed as customers didn't want to stay at an inn known to have been the scene of a brutal fight.
Nakaoka reveals that he has a photograph of the man calling himself Ryōma Sakamoto and Saitō reveals that it is the man he considers his brother, Hanpeita Takechi. It is decided that Nakaoka will talk with Kichinosuke Saigō while Todō talks to Ikumatsu at Matsunoi so that he can meet with Kogoru Katsura.
That night, Nakaoka arrives at Saitō's room at Teradaya to let him know his meeting with Saigō was successful. Todō hadn't arrived yet, so Nakaoka and Saitō planned to talk to Ikumatsu themselves, however, when they head downstairs they find Todō, who is slowly dying. Ikumatsu said that Katsura said he was on for the meeting, but Takeda saw Todō and wounded him.
Saitō arrived at Matsunoi only to find that Takeda held Ikumatsu hostage and wanted Saitō to contact Katsura so that he could join the Choshu Domain. Saitō instead fights and slays Takeda due to his sexual assault on Ikumatsu.
The remaining Shinsengumi members bring Todō's body, at the behest of his dying words, to the scene so that it would look like Todō and Takeda fought to the death. This would keep Todō's secret so the meeting could go on.
Oryo lights a fire in the Omiya inn, signaling that the Shinsengumi can proceed with their plan. They battle their way through the warriors and Saitō arrives by himself at the meeting site. Nakaoka lay wounded on the floor and let Saitō know it was a setup because Hanpeita Takechi was aware of their plan in advance.
Tadasaburô Sasaki, Ito Kashitaro, and a visibly aged Hanpeita Takechi teamed up. The former stop Saitō from going after the latter. All three leave and Hanpeita tells Saitō to come to Tosa.
The other Shinsengumi captains arrive afterward and Saitō tells them that Hanpeita said to go to Tosa. An unknown dead man had been dressed as the imposter Ryōma by Tadasaburô, Ito, and Hanpeita. Saitō decides to continue using his assumed name, letting history record that Ryōma Sakamoto died that night.
After waking in the morning Saitō spends the entire day taking Oryo to establishments around Kyo. Oryo tells him to promise her that he will return to Kyo after he settles things in Tosa, and Saitō gives her his word.
Saitô, Hijikata, Okita, and Nagakura arrive by boat in Tosa, only to see that it has been heavily fortified for war. They battle their way through and are confronted by the head of the Mimawarigumi, Tadasaburo Sasaki. They defeat him, but he comes back for more. Nagakura stays back to hold them off while the other three captains press forward. After fighting more enemies, they are confronted by Ito Kashitaro. They battle and win, but he also comes back for more. This time Hijikata stays to hold them off, and the remaining two captains fight through more enemies. They are confronted by Thomas Glover, the Englishman who has been supplying Hanpeita Takechi with weapons. They defeat him, he also keeps fighting, and Okita stays behind.
Saitô fights through the remaining enemies alone until he finally reaches Hanpeita Takechi. They battle, and Saitô wins, but he refuses to slay his brother. Takechi reveals that Tōyō Yoshida wanted to leave the Tosa loyalist party to Ryōma and he resented that. He felt that his foster father was weak because he wanted to spare as many lives as possible. Takechi did everything he did because he truly thought he could save Japan by tearing it down. He admits that seeing everything that Saitô did, including restoring the emperor and the Imperial court to power, without taking too many lives revealed that he was wrong. He truly believes now that Tōyō was right.
After the two brothers reconcile, Yodo Yamauchi, the daimyo of the Tosa domain, shoots Takechi. It is revealed that he used Hanpeita Takechi to weaken Japan so that he could give it to the British. Once it became a British colony, he would become the next ruler of Japan.
He shoots Saitô, but he just brushes it aside and comes towards him. Yodo unloads his gun on Saitô, but he still comes forward. He stops gloating when he realizes he is no match for the stronger man. Hijikata, Okita, and Nagakura arrive, and together with Saitô, they slay the cowardly Yodo.
Saitô remains in his assumed identity, while Takechi takes on the identity of Yodo Yamauchi. Over the course of a year, Takechi uses Yodo's authority to undo all the harm the real Yodo did to the country. Nakaoka Shintarō survived his wounds and has remained at the inn writing the biography of Ryôma Sakamoto. Otose now runs the inn without Oryo as she has left Kyo to spend the rest of her life with Saitô.
