The prestigious private school, Cross Academy, consists of two sessions, the Day Class and Night Class. Although the Night Class consists of students that are all beautiful, intelligent elites, they are in fact vampires!

Tomorrow is the annual St. Xocolatl's Day, when it is customary for the girls at the academy to give chocolates to the boys. Although Yuki is busy patrolling the school grounds to catch the Day Class girls trying to sneak chocolates to the Night Class boys the day before the event, she finds time to make chocolates for Kaname as her token of appreciation.

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.

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.

Zero tried to sink his fangs into Yuki, but he was able to get hold of himself just before he succumbed to his urge. However, there is someone who is trying to kill him: the new teacher Yagari.

Yuki makes a secret decision regarding Zero, who is now determined to fight his affliction until the very end. Yuki feels guilty for betraying Kaname and keeping a secret from him.

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 and Zero are busy dealing with the Day Class students who are chasing after the Night Class students more fervently than ever due to the upcoming dance.

To prepare for the upcoming exam, Zero tutors Yuki, but all the while, she notices something wrong with him. Meanwhile, at the Moon Dormitory, Kaname confronts Maria in his room.

Maria's masked servant is none other than Zero's twin brother, Ichiru, whom Zero has not seen since their separation long ago.

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.

After suffering a mortal wound, Shizuka quietly dies in Ichiru's arms. Meanwhile, Yuki and Zero try to find where Shizuka may have gone, but Zero is constantly thwarted by his Level E seizures.