The prestigious private school, Cross Academy, consists of a Day Class of human students and a Night Class of vampires. The peace is kept by the Disciplinary Committee, Yuki Cross and Zero Kiryu. Yuki's earliest memories are of being attacked by a vampire and saved by another vampire, Kaname Kuran, who is now dorm president of the Night Class.
Tomorrow is the annual St. Xocolatl's Day when it is customary for girls to give chocolates to boys, which means extra work for Cross Academy's Disciplinary Committee. Yuki still finds time to make chocolates for Kaname. Meanwhile, Zero struggles with the blood tablets.
As a duty of the Disciplinary Committee, Yuki and Zero must conduct a surprise inspection of the students' belongings at both the Sun and the Moon Dormitories. Just as they are about to enter the Moon Dormitory, Zero suddenly leaves the school grounds. Yuki goes after him in a panic but can't find him. As she roams the streets by herself, Yuki is haunted by her memories from ten years ago, when suddenly a mysterious mother and child appear before her...
Seeing the state Yuki is in, Kaname takes her from Zero, who is left speechless when he realizes what he has done. Yuki cries in frustration, unaware of Zero's secret, even though they've known each other for a long time. Later, she overhears the conversation between the Headmaster and Kaname at the Headmaster's office. "In order to protect Zero..." After much consideration, Yuki heads to the Moon Dormitory to ask a certain favor of Kaname...
A new ethics teacher, Toga Yagari, arrives at Cross Academy. His looks, which are atypical for a teacher, are all the buzz among the Day Class students, and even Zero seems to have lost his usual composure. Upon hearing a question directed to Yagari from one of the students, Zero suddenly leaves the classroom. Yuki hurries after him to ask about his relationship with Yagari, but Zero refuses to answer...
There is a rare commotion in the Moon Dormitory when the Night Class gets word that Takuma's grandfather will be visiting. Takuma's grandfather, nicknamed Ichio, is an important figure in the vampire world and is feared by many...
Yuki learns that Maria's true identity is Shizuka, the pureblood vampire who bit Zero and turned him into a vampire. With this information, Yuki accepts a deal from Shizuka and offers her blood in order to save Zero...
Yuki has a lot on her mind after almost being kissed by Zero. She asserts that she will not speak to Kaname until he admits to Zero's innocence. While walking around town with Sayori, she comes across a lost little boy.
While the Night Class is at the Aido family's vacation home, Yuki, driven by her desire to stop hurting Zero, tries to regain her memory of the past and becomes haunted by even more powerful visions.
Yuki is continually haunted by visions of blood. Nevertheless, she is determined to find out about her past from Kaname, but he repeatedly evades her question. Zero sees Yuki looking troubled and goes to the Moon Dormitory by himself.
Senri returns to the Academy, but upon having a confidential talk with Ichiru, he becomes noticeably different from before. The insolent Senri goes to see Ruka who has been locked up in her room since she got word of Kaname's new girlfriend.
Absorbing Kaname's blood finally revives Rido. The vampires all suspect this, and an unsettled mood enshrouds the Academy. The Headmaster calls for an emergency evacuation of the Day Class students, as Rido's servant vampires begin attacking the students.
In order to protect the academy, the Headmaster confronts the head of the Hunter Society while Rido is still on the rampage. In the meantime, Ichiru pays a visit to Zero and shoots him with the Bloody Rose gun.
Yuki understands the position she has been put in, and remembering Kaname's words, "Do what you have to do," Yuki decides that as Guardian, she must protect all the students at the academy and fight Rido.
All of Zero's strength is not enough to kill Rido, and Rido runs away. However, Kaname finds Rido, and Zero arrives soon after. The two of them attack Rido. After the fight, the sun rises upon the devastated Cross Academy.