A large portion of the students are missing after the last battle. Haruka and Yukino look for Shizuru, and find her with Natsuki, who Shizuru has been inappropriately touching while she sleeps. Mai goes in search of the Black Prince to learn if killing the other HiME's Children will give her the power to bring back Takumi.
Mai shows up late for class, to Mikoto's delight. Midori organizes the HiMEs into the HiME Rangers, and takes them out to karaoke to bond. Takumi discovers Akira's true identity and she must kill him. Afterwards, Nagi tells them that there will be no more Orphans; now they must fight each other's Children. The HiME's Carnival had just begun.
Joseph Greer, Miyu, and Alyssa Searrs are working for the Searrs Foundation. They kidnap Natsuki, and Yukino Kikukawa, who is a HiME, uses her powers to find her. Mai and Mikoto go to rescue her, and save her from Miyu and Alyssa Searrs. In the end, Alyssa takes over control of the operation from Greer.
A vampire is stalking the campus. It removes girls' clothing and drinks their blood trying to determine if they are HiMEs. Nagi tells Mai not to get involved with it, since there appears to be another group looking to use the HiME. The school's nun, Yukariko Sanada, turns out to be a HiME and defeats it.
The school holds a festival. Akane Higurashi fights an Orphan to protect her boyfriend Kazuya, but Miyu Greer kills Akane's Child, and Kazuya dies. Nagi Homura explains that the life of the person who's most important to the HiME is forfeit, not the HiME's life as Akane thought. Mai fights with Kagutsuchi for the second time, and reveals her powers to Reito.