Jiyu Nanohana, a fourteen-year old junior highschool student who attends Hontsuru Jr.High unexpectedly meets Koinosuke Odago, an assistant of Yagyu Jubei who has searched 300 years for a worthy successor for the Lovely Eyepatch. He implores Jiyu to accept the Eyepatch but she steadfastly refuses.

The problem between Jiyu and Koinosuke continues as a new assassin arrives to eliminate Yagyu Jubei II.

The conflict continues when two new assassins arrive, takes the form of Jiyu's new teachers. They challenge her to a duel but is badly defeated, but Bantaro is injured during their fight.

Bantaro was cured by Shiro's mother. As things begin back to normal, Hajime appears and asks Shiro to join their clan; Shiro explains that he as no intentions of doing so, but Hajime reminds him that he knows Shiro has a longing to fight Jubei II and leaves. He then accompanies Jiyu and asks her about the Eyepatch, she says it is nothing and throws it away.

In order to release Jiyu from the burden of becoming Yagyu Jubei and being targeted by the Ryujoji, Shiro challenges her to a duel. Later, Jiyu meets a Ryujoji assassin, he explains their 300-year old grudge and goal to her.

Jubei II defeats the assassins. Afterward, Shiro and Jubei II engage in a duel, he cuts off the Eyepatch, but as soon as Jiyu returns to her normal self, she collapses. Bantaro takes her to a doctor while Hajime attacks Shiro, and takes the Eyepatch.

Jiyu is resting in Shiro's house. Sai tries to cool her down and remembers the memories of his deceased wife.

Back to Hajime's hideout, he has not discovered the power of the Eyepatch, thus, he orders his men to go get Jiyu. Meanwhile, the Nanohanas is having a party, Mikage appears during the show and tells Jiyu about their changed lives.

Jiyu along with Koinosuke and the Ruffians are being held hostages, Hajime tortures her friends, forcing her to tell him the power of the Eyepatch. Shiro appears and fights him, Hajime is defeated by Jubei II. When Shiro goes back and thanks the old teacher, it turns out that he became possessed by Taiko Daiyu's spirit.

Mikage while exploring the Ryujoji's hideout, she was attacked by Shiro/Taiko Daiyu and was heavily injured. Sai finds her Mikage stumbles out and collapses in front of him. He brings her home, treats her and then hugs her, but Jiyu sees everything and runs off. Mikage tells him to protect Jiyu and that the Ryujoji grudge lives on. As soon as she runs outside, a possessed Shiro appears and attacks her.

The fight between the possessed Shiro and Jubei II continues as Sai tries to stop them. Jubei II however, says that she has to end this grudge and Jiyu's soul will rest in her eternally.

While Jubei II fights Shiro/Taiko Daiyu, Koinosuke explains everything to the rest. Jubei II is exhausted and nearly killed by Taiko Daiyu, but Shiro takes over his body and holds back the thrust. Jubei defeats him and Taiko Daiyu's spirit leaves the body. She tells everyone that she cannot return when Taiko Daiyu still exists. Sai lets him to take over his body and fights Jubei. During their battle, Sai's spirit jumps out and grab his daughter's spirit while Jubei II destroy Taiko Daiyu. Though they have won the battle, but Koinosuke left. A few days later, the heroes celebrate the formation of The New Student Lovelies, Jiyu looks at the Koinosuke whistle and says she'll blow on it when she wants to see him.