The Shinsegumi wait to see if Sannan-san recovers from his violent reaction to "that medicine" - and work to keep Itou from noticing. Chizuru has a fuller truth revealed to her because of the incident. While on patrol, she and the soldiers rescue a young woman who looks almost exactly like Chizuru, who still dresses like a boy. Later, as the Shinsengumi take up guard duty for the Shōgun's visit, the three strangers - calling themselves "Oni" - try to kidnap Chizuru.

Koudou Yukimura disappears after a fire, and Nimi soon joins him along with all of the research on the Water of Life. The Roshigumi put forth all their efforts in attempt to find him.

Chizuru has been depressed thinking about what Kazama said before he was chased off; her friends set up an afternoon with the charming Osen-chan to cheer her up. Hijikata and Shinpachi have a confrontation. The Shinsengumi get bad news from the Bakufu; during a related assignment, they get an unpleasant and unsettling surprise. With the reward money for the successful assignment, however, they finally get Chizuru dressed up like a girl during a rowdy celebratory night out. The princess gets a report.

The Oni are foiled and vanish again. Chizuru makes friends with Sen, whom she rescues again from thugs. The Shinsengumi members undergo medical exams - and the doctor giving the physicals is a friend of Chizuru's father. His prescription: Clean the HQ! Chizuru finds out a terrible secret about Okita. Dr. Matsumoto also fills Chizuru in on some more details about the ochimizu and Rasetsu. Kazama gets into the headquarters to confront Chizuru again, and is later reproved by Amagiri for his interference with humans.

After several months, Chizuru's service to the Shinsegumi has become a regular part of their everyday lives. Itou Kashitarou allies with the corps as an advisor, but not all the soldiers are happy with his presence. The Shinsengumi make plans to move to a larger headquarters. Meanwhile, Yamanami, discontented with his ability to contribute, continues research on "that medicine" in a dangerous way.

The anticipation of murder and mutiny rises until the storm breaks. And Ryunosuke's true loyalty is put to the test.

After Vice Commander Hijikata rebukes Souji Okita for his aggressiveness, Ryunosuke learns about the young warrior's past. Meanwhile, Serizawa provokes Souji into satisfying his desire for blood.

Itou seeks to subvert and split the Shinsengumi, especially after he finds out Yamanami is still alive. Chizuru still hides her quick-healing ability when she is injured by an ochimizu-maddened soldier. Osen and her kunoichi Kimigiku come to collect Chizuru from the Shinsengumi headquarters for her own safety; Osen claims an ancient oni bloodline and forces Chizuru to admit her own oni status. The Rasetsu Squad are activated when Kazura attempts yet again to kidnap Chizuru from the headquarters.

The smaller squad of Shinsengumi out to apprehend the Choushuu conspirators find them at Ikedaya. Chizuru is sent with Yamazaki to update the other soldiers surveilling at Shikokuya so they can reinforce their brethren, but runs the message herself while Yamazaki fights off attackers. Back upstairs at Ikedaya, Okita and Heisuke engage with two mysterious and very powerful strangers. The Ikedaya Incident leads to a request for the Shinsengumi to fight on the front lines - the beginning of the Kinmon no Hen Incident.

Hijikata's army has a few victories in Futamata-guchi, but Ootori's army falls in Matsumae-guchi. Hijikata and his army is forced to retreat before the enemies arrive. When another blood thirst strikes, he realizes that his body cannot hold out much longer. In Benten Daiba, Hijikata meets up with Shimada and Ootori, who blames himself for the loss at Matsumae-guchi. Hijikata tells him that it wasn't his fault and shakes his hand in the end. Later when they are alone, Hijikata ends up confessing to Chizuru and kissing her. When the New Government Army attacks Benten Daiba, Hijikata is shot while on horseback. Refusing to let him die, Chizuru gives him some of her blood. While attempting to go back to Goryoukaku, Kazama Chikage appears under a beautiful cherry blossom tree. Kazama declares Hijikata not a Rasetsu, but an Oni. He gives Hijikata an Oni name--"Hakuouki" meaning pale sakura oni.They fight and Hijikata kills Kazama. Hijikata is shown unconscious in the last few minutes of the episode but he does not die because he did not turn into ashes and disappear. Chizuru did however hallucinate the fact that he wiped her tears and whispered her name. Regardless Hijikata did not die in the last episode.

Bleeding and left to die, Ryunosuke Ibuki is rescued and taken in by the Roshigumi - a band of warriors struggling to find a sponsor and make a name for themselves in Kyoto. Unfortunately, Ryunosuke can't easily pay off a life debt..

Hajime Saito recalls his early days at the dojo. He offers to teach Ryunosuke sword fighting. Meanwhile, the Roshigumi's reputation fails due to misinterpretations and debts.

Spreading renown is no easy task with an unruly commander. The other Roshigumi commanders attempt to curb Serizawa with a strict set of rules, but he is not moved. Meanwhile, his bloodthirsty attributes rub off on a certain young warrior.

The feuds with Serizawa continue; Commander Kondou and Vice Commander Hijikata reminisce about their past and contemplate their goals. Meanwhile, the experiments on the strange Water of Life proceed.

Commander Serizawa has no bonds. The research on the Water of Life advances. And the Mibu Roshigumi receive the chance of a lifetime to make a name for themselves.

A mysterious skilled warrior joins the Roshigumi. Meanwhile, Ryunosuke is unable to even draw his sword. He learns more about the Roshigumi, including shocking information regarding his own benefactor, Commander Kamo Serizawa.

Okita's tuberculosis is getting worse, and Hijikata refuses to let him accompany the rest, telling him to get better first. The troops leave Kondou in Hino, and proceed on. Nagakura shows disagreement with Kondou's actions, and Saito asks Hijikata if he think that they can win the battle. Hijikata replies that in their current state, they cannot match the enemy. Later, Chizuru has a nightmare and follows Saito outside the camp, where he tells her about his past and his opinions. They meet up a messenger, who tells them that the enemy has already entered Koufu Castle. Kondou refuses to let the army retreat, and Hijikata leaves to find more troops. Before he leaves, he makes a "Chiming Metal" oath with Chizuru, making her promise to stay alive and protect Kondou. Meanwhile, Kaoru talks to a mysterious man. The war starts just a few hours after Hijikata leaves, and Kondou agrees to forfeit after seeing the many men he let die in vain. Nagakura and Harada run into the Oni from before, and battle a strange group of Rasetsu. It is revealed that the creator of the Rasetsu is Chizuru's father, Koudou.

Shiranui, Harada, and Nagakura fight the Rasetsu, but there are too many of them. Shiranui uses his last bullet to blow up a cart of explosive material, allowing the Shinsengumi to escape. Kondou and Chizuru escape into the forest, but are confronted by Kaoru, who reveals his relationship to Chizuru. Chizuru refuses his offer to leave with him, and draws her sword against him which shocks Kaoru. She is almost killed by Kaoru but Okita interrupts him. He tries to defeat Kaoru, but fails. Kazama appears and kills Kaoru. The Shinsengumi moves into residences at Hatamoto, and Harada takes Chizuru out to eat dango, and they bring some back for Okita. Hijikata comes back to Edo with new troops, and Harada and Nagakura leave the Shinsengumi to fight the Satsuma and Choushuu in their own way.

Saito leads the Shinsengumi into the Battle in Aizu. He is sent to command Masaki, a young Aizu Clan soldier, and his men. Masaki refuses to obey his orders, believing that Saito is not a warrior since he wears his swords and clothes differently. The Shinsengumi and Masaki's army attack at Shirakawa-guchi, but are forced to retreat. Later, Masaki acknowledges Saito's status as a warrior. Hijikata recovers enough to return to the Shinsengumi. They decide to attack at Bonari Pass, and again they are completely outnumbered. Masaki sacrifices himself so Saito and the Shinsengumi can retreat. The lord of the Aizu orders them to retreat to Sendai to get reinforcements while he stays behind. Saito decides to stay with the Aizu Clan and fly the Shinsengumi's banner.

Chizuru Yukimura is a young woman who, disguised as a boy, traveled to Kyoto to search for her missing father. However, she is attacked by ronin. Just as one of the ronin is about to find her hiding place, he is attacked by demons. The demons close in on Chizuru, when she is saved by the Shinsengumi. In Shinsengumi headquarters, she explains who she is and why she is there. The Shinsengumi allow her to stay as they are looking for her father as well.