First Arc
Shizuka Hio
At the beginning of the manga, Kaien is portrayed as the goofy headmaster of Cross Academy and adopted father to Yuki and Zero. While he seems to be aware of what is going on at the school at all times, he leaves the enforcement of school discipline to Yuki and Zero. After Zero completely awakens as a vampire, it is revealed that Kaien knew the truth behind the deaths of Zero's parents all along and that he had been the one to take Zero to get his tattoo in the hopes that it would slow down Zero's transformation into a vampire. Kaien performs the ceremony to have Yuki tame Zero.
Yuki's secret
Later on, after Yuki's memories of her past begin to awaken, Kaien accompanies Yuki and Zero to the Hunter Association's main headquarters in order to look up the records on Yuki's history. While there, Yuki accidentally discovers Kaien was once a Vampire Hunter, a fact which does not surprise Yuki; however, Kaien states he is ashamed for having killed vampires in the past and didn't want her to know. Yuki responds that he is her father and nothing has changed.
Rido's return
Once Yuki's memories finally return and she reawakens as aPureblood vampire , Kaien admits, to a disgusted Zero, that he knew everything about her past but kept stayed silent. When the school is subsequently attacked by Rido's legion of vampires, Kaien attempts to maintain order, but it is not until the Hunters arrive that he, along with Yagari, go out to defend the Night Class, declaring that while the Night Class is protecting the human students, he will protect the Night Class. During this battle, Kaien fights and kills the acting president of the Hunters Association, discovering in the process that the president had been slowly transforming into a vampire after drinking the blood of powerful vampires. After the battle ends, the Hunters take Kaien into custody in an effort to hold him accountable for failing to keep the school safe.
Second Arc
A year later
Kaien was held by the Hunter's Association, but eventually they decided to let him go to see how things went. Kaien returns to recruit Zero as the future president of the Hunter's Association, a role that he will fulfill until Zero takes over. He also returns to Cross Academy as the head of the school. Concerned for the well being of both of his children, Kaien tells Zero that he will stand between them should it ever become necessary.
Hunter and Vampire peace?
Kaien attends the meeting between the Vampire Hunters and Kaname. Kaien expresses doubts over the way Kaname dealt with the former Vampire Council, believing it to be too harsh, and at risk of alienating the other vampires, in particular the other Purebloods. He also questions whether or not Kaname will be able to keep the rest of vampire society in line, to which Kaname responds that the answer to his question will be in how many vampires choose to attend the ball being given in honor of the continued cooperation between the Hunters and the Vampire Society.
It is at the ball that Kaien and Yuki are finally reunited, though the two are unable to speak with one another, much to Kaien's displeasure. After the mysterious death of Ouri, a Pureblood attending the ball, at the hands of a Vampire Hunter who was turned into a vampire and then forced to kill him, Kaien, along with Zero, takes the lead in the investigation. Nominally determined to have been a suicide, Kaien declares that the Hunters must never let this sort of thing happen again.
Kaien is later seen in Isaya's house, just after Yuki's visit with him. When Isaya asks why Kaien didn't greet her before she left, he responds that it's fine since he didn't want her knowing that they were old friends, in case it influenced her way of seeing things. Kaien also remarks on how much Yuki has come to resemble her mother, but clarifies that he does not hold romantic feelings for Yuki at all. When Isaya comments that seeing Kaien as a father is something he never could have imagined, that he'd always thought Kaien would remain a neutral spectator just as he himself is, Kaien responds that by opening the school and caring for Yuki, he realized he could make a difference. He thinks that it is important that Yuki grew up watching that.
Kaname's plans
Shortly after Kaname attacks the Pureblood Toma, Zero brings Hanabusa Aido into Vampire Hunter Headquarters for questioning about Kaname's plans. Unable to get any information out of Aidou, Kaien decides to return him to Kuran manor. On the way home, the two are unexpectedly flagged down by Yuki who insists they drive to the Hanadagi family manor. Upon arriving at the scene, Yuki, Aidou, and Kaien witness Kaname beheading Aido's father after having killed the Pureblood Hanadagi. Kaien attempts to pursue Kaname after the death of Nagamichi Aido; however, Kaname escapes. Kaien then encounters a distraught Yuki who insists on following after Kaname. Kaien tells her that as her adoptive parent, he is unable to allow her to follow after Kaname due to his inexplicable actions.
Return of the Night Class
After returning to Vampire Hunter Headquarters with Yuki and Aido, Kaien questions Yuki about Kaname's plans. Unable to provide any information, Kaien agrees to allow Yuki to take the lead in attempting to track down Kaname for questioning in the murder of Nagamichi Aido. Kaien also agrees to allow Yuki to assist in hunting down vampires and in recreating the Night Class.