Yuuki Cross' earliest memory is of being all alone on a snowy night in winter, when she was attacked by an evil "Level E" vampire and saved by a powerful but kind vampire named Kaname Kuran. Afterward, Yuuki is then brought to Kaien Cross, who adopts her. Kaien Cross is the Headmaster of Cross Academy and is also an ex-vampire hunter who now wishes for vampires and humans to live alongside peacefully. Yuuki grows up to become a prefect AKA: "guardian" for the school, which is running an experimental program that is trying to prove that vampires can coexist peacefully with humans. The human students of the "Day Class" are not aware that their counterparts in the "Night Class" are all actually vampires. Only the prefects know the truth.
The Night Class student body is made up of upper-class vampires, as there is a hierarchy among vampire society. "Purebloods" (Level A) are the rarest and most elite, having never mixed with humans in their ancestry. They are also the most powerful and their blood is the most desirable as it grants whoever drinks it greater powers. Purebloods are also the only class of vampire with the power to turn humans into other vampires. Kaname is the only pureblood within the night class, though a few others are introduced throughout the series. The other students are "nobles" AKA: "aristocrats" whose bloodlines have only slightly mixed with humans. They are still very powerful however, but not as powerful as purebloods. Then there are 'normal' vampires (level C). And finally, there are the lower classes of vampires (level E) that consist of humans who have been changed into vampires- not born as one. These types of vampires eventually go insane with bloodlust unless they are stabilized by drinking the blood of the one who originally bit them. Level E vampires are almost always beyond help, losing all their rationality and killing without remorse to get blood.
Yuuki's fellow guardian and childhood companion, Zero Kiryu, whose parents were killed in front of him by a pureblood vampire four years earlier, is now determined to kill all purebloods and refuses to trust the other vampires at the school. Zero himself is now manifesting vampire traits however, having been bitten that day by the same vampire who attacked his family, Shizuka Hio. Due to his horrific past and the fact that he came from a family of vampire hunters, he hates what he has become and fights his instincts the best he can.
Yuuki tries to help him fight his bloodlust while also seeking to recover the memories she lost as a young child. As the series progresses, Zero's thirst for blood leads to his drinking from Yuuki, by her consent, to avoid becoming a level E vampire and losing himself to his monstrous instincts. Kaname is very protective of Yuuki, and to stop her from having to do this, he gives Zero his own "pure" blood. Also, since he had consumed the blood of Shizuka Hio, his own helps keep Zero from going insane and from needing to feed from Yuuki.
Eventually, it is revealed that Yuuki is a pureblood vampire herself; the Pureblood Princess of the Kuran family, who had been transformed into a human before she lost her memories. It is also revealed that Kaname is Yuuki's older brother and that they spent their childhood together. They were also apparently meant to be married and were technically engaged as children, a practice common among purebloods to preserve bloodlines. Despite this, Kaname is not Yuuki's true blood brother, but an ancient and powerful ancestor of the royal Kuran family who was resurrected by Rido Kuran. He was raised by Yuuki's parents, Juuri and Haruka Kuran, after Rido had kidnapped and sacrificed their first child to bring him back to life. To save Yuuki from being killed by her evil uncle Rido, her mother sacrificed her life in order to perform a spell that would seal Yuuki's memories and allow her to live as a human in order to avoid being found.
After Yuuki reawakens to her vampire nature, Rido again tries to kill her and consume her power. As Kaname kills the corrupt vampire senate who they had discovered were working together with their uncle, Yuuki fights Rido. During a fierce battle, Zero aids her in killing him, but later on tells her he will have to kill her when he sees her once again, since she is a pureblood. She tells him that she will keep running, so that he will have a reason to live. Although this is where the anime ends, the manga continues the story and is updated monthly in LaLa Magazine.