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.

Chizuru starts to work her way into the Shinsengumi's society, motivated by a desire to be useful and concern over the injured Sannen-san. She gains permission to leave headquarters in the company of the regular patrols, in order to continue the search for her father. Following one lead, she runs headlong into the Shinsengumi's enemies, and in the subsequent fight, the Shinsengumi learn of a Choushuu plot against Kyoto and the Emperor.

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.

A mysterious princess is introduced, speaking of a "storm" arising. Meanwhile, the Shisengumi have marched to the front lines, and leap into battle on their own accord. Cleaning up after an enemy sortie, Saitou finds one of the mystery men from Ikedaya (Amagiri Kyuuju) defending Satsuma Clan soldiers; Harada encounters a third powerful stranger (Shiranui Kyou) wielding a Western-style handgun; and Hijikata with Chizuru are confronted by the blond stranger (Chikage Kazama) as they race to Mt. Tennozan.

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 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.

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.

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.

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 Shinsengumi learn of Itou's plot to assassinate Commander Kondou. The Shinsengumi is dispatched to Itou's compound, in spite of concerns over Heisuke's safety. After Itou is assassinated, Saito and Chizuru confront Heisuke directly, and persuade him to fight alongside them against Itou's men. Meanwhile Souji, severely weakened by his tuberculosis, is approached by Kaoru, who reveals his true identity and offers him a vial of the "medicine" that would heal him and make him a Rasetsu. Back at Itou's compound, the Shinsengumi forces are surrounded by Itou's men, Shiranui, and Amagiri. Heisuke engages Amagiri in battle, and is brutally attacked.

After his brutal defeat, Heisuke drinks Ochimizu and becomes a Rasetsu. An attempted assassination leaves Captain Kondou in critical condition. In order to avenge Kondou, Okita drinks the Ochimizu that Kaoru gave him, also becoming a Rasetsu. Kaoru appears, and reveals that the Ochimizu will not heal his tuberculosis. He also reveals the reason he hates Chizuru. In an ensuing battle, Okita manages to kill Kondou's attackers, but is also heavily wounded by gunfire. With both Okita and Kondou close to death, Hijikata sends them to Osaka Castle to be treated by Doctor Matsumoto.

The conflict between the Shinsengumi and imperialist forces breaks out into the Boshin War. During the Battle of Toba-Fushimi, Inoue is brutally murdered in front of Chizuru. Kazama appears and kills Inoue's murderers. Hijikata engages Kazama in battle, believing that he killed Inoue. During the fight, Hijikata drinks Ochimizu and becomes a Rasetsu to better his odds of victory. Yamazaki steps in and is grievously wounded. The fierce battle ends abruptly when Amagiri comes to collect Kazama. In the aftermath, the Shinsengumi bury the dead before departing by ship for Edo. En route, Yamazaki succumbs to his wounds and is buried at sea.