The story takes place in Japan in the early 21st century, in an alternate reality where the Tokugawa Shogunate has remained in power. In this reality, student councils are tasked with oppressing schools. Yagyuu Muneakira is a high school student who rebels against his student council with the help of girls who've had the names of famous samurai heroes passed on to them.
Four mysterious shadows revealed to be Dark Samurai appear within a cemetery and are greeted by Charles who engages them in battle. Muneakira returns to the Yagyu Dojo from his training away only to find that the dojo has been turned into the Shinkage Maid Cafe (True Shadow Maid Cafe). Yukimura reveals that due to the Reiman Shock, the dojo had to make money or else it'd be repossessed. Kanetsugu is shown to have been sent out to the cemetery to hand out flyers where she meets the Dark Samurai and directs them to the dojo. The Dark Samurai skirmish against Muneakira, Yukimura and Sen leaving Muneakira's General's powers sealed. Muneakira is given a month to bring back the Master Samurai Jubei or else his General powers will be destroyed. To the shock of everyone, Musashi returns the next day simply as a customer with an entirely different demeanor.
A mysterious underwear thief lurks the Café terrorizing the Maidens...
Kanetsugu introduces the Battle for the title of Number One Maid in a malevolent attempt to get rid of Sasuke.
Gisen visits the Café and tries to apply for a Job.
The Café is in trouble when new Maiden Cafés opened in the area stealing the clientele. The M-1 Grand Prix tournament hopes to return Maiden balance to the Number One Café...
With the Maidens Café closed and the Dojo debt paid off, the girls can concentrate on their "qi" training.
Keiji continue to train the girls in the arts of "qi". Jubei is stuck in master samurai mode and her "qi" is fading fast.
Yukimura and Matabei are assaulted while returning from research into the Samurai Bible by an unknown assailant who is driven off by Inshun. The next day Hanzo and Matabei are regretful that they can't protect their masters during conflicts in the past. Everyone in the dojo have a meeting about the unknown assailant while Satchin and Jubei continue their Ki training in which Satchin runs across Inshun. Jubei takes Inshun along to spend time with her for the day during which she gives her the nickname Inko-chan. They both agree to be friends after the upcoming battle. That night Muneakira, Jubei, Yukimura, Sen, Matabei, and Hanzo go searching for the mysterious assailant. Sen is attacked during the search but Hanzo is unable to protect her. Only through Inzo's intervention is the assailant driven off but the group mistakes Inzo as the actual assailant.
Mataemon attacks Kojiro under external influence as Yoshihiko watches the repair of the barrier protecting the Chingo Stone. As Sen, Muneakira, and Yukimura discuss the the situation, Jubei attempts to defend Inshun from suspicion leading to her running away. Yukimura continues researching the Samurai Bride, Sen goes out for training and Matabei trains with Hanzo in kissing. Kanetsugu interrupts the latter two to train them but her plan backfires as Matabei and Hanzo both torture her during their fantasies about kissing. Jubei talks to Musashi about her concerns that everyone thinks that Inshun is the street attacker unknowingly raising Musashi's suspicions. Kojiro watches as Mataemon is controlled and follows her back into town. Muneakira, Sen, Yukimura, Matabei, and Hanzo search the town while Musashi confronts a silent Inshun about being the street attacker. Detecting the street attacker, Sen retreats back to the forest surrounding the dojo only to be captured.
Kojiro questions the ghost in the cemetery about the reason for the revival of the Dark Samurai; Matabei, Hanzo, Kanetsugu and Gisen wait in the dojo; and Muneakira, Jubei, Jubei, and Yukimura question Sen about the Chingo Stone. It's revealed that the Chingo Stone lies at the base of Mt Fuji and controls Japan's accumulation of ki thus protecting it from unstable ki. Great Japan was founded by the Chingo Stone being placed there and is continually held together by the stone, however the ghost wishes to use the Dark Samurai to destroy the Chingo Stone. The ghost's only desire is for war due to their unapproval of the Tokugawa's power. Yoshihiko's master samurai have thus far stopped them but in their defeat against the Dark Samurai, Charles dropped the name of Jubei as the real identity of the one who defeated Amakusa. This gave Yoshihiko a month for repairs but the ghost was angry because Musashi got hung up on the battle allowing Yoshihiko that time.
Muneakira and his Master Samurai are attempting to create the Samurai Bride with flashbacks intervening of their conversation after Yukimura revealed the conditions. Due to the sealing by Musashi, Muneakira is unable to continue. Inshun asks Musashi to give Muneakira the method to unseal himself after the battle and disappears while Kojiro talks to Mataemon about the flaws each Dark Samurai possesses due to improper resurrection. While Musashi goes to Yagyu Dojo for the battle, Kojiro and Mataemon attack the Chingo Stone. Jubei provokes Musashi into battle while Inshun defends the Chingo Stone. Inshun is taken down by Mataemon as the ghosts within the cemetery grow stronger due to the damage inflicted upon the Chingo Stone. As Kojiro is about to kill Charles, Gisen appears using her Devil's Eye. Kojiro and Mataemon are able to flee but as the ghosts empower Musashi, she threatens to kill herself since she can't fight fair against Jubei.
Sen blindly pursues the cursed spirit as it arrives at the Academy with Hanzo sacrificing herself to protect Sen. Distraught, Sen is also killed as she remorses over Hanzo's body. Both are absorbed by the spirit as Yukimura, Matabei, Sasuke and Kanetsugu continue to fight. They are also killed and absorbed one by one as Muneakira, Jubei, and Keiji arrive to witness their absorbtion. Muneakira attacks the spirit only to be saved by Keiji as he is hit. Enraged Jubei enters into the spirit meeting with Inko who tells her she wishes to die by Jubei's hand and that it is possible as Muneakira is still alive. Within the Academy, Yoshihiko is informed that the spirit will arrive seven minutes before the Chingo Stone's barrier is complete. Keiji pours her ki into Muneakira telling Jubei that while everyone else believes that the Samurai Bride is monstrously powerful, she believes that a Samurai Bride isn't.
