Tomoya Okazaki is a third year high school student resentful of his life. His mother passed away from a car accident when he was younger, causing his father to resort to alcohol and gambling. This results in fights between the two until Tomoya's shoulder is injured in a fight. Since then, Tomoya has had distant relationships with his father, causing him to become a delinquent over time. While on a walk to school, he meets a strange girl named Nagisa Furukawa who is a year older, but is repeating due to illness. Due to this, she is often alone as most of her friends have moved on. The two begin hanging out and slowly, as time goes by, Tomoya finds his life shifting in a new direction.
Yoshitaka Nakabayashi, a 14-year-old millionaire who got this huge inheritance after his parents died in an accident, found himself needed to be taken care of and tried to hire live-in maids to do the job. Two runaway girls, Izumi Sawatari and her younger sister Mitsuki, stumped into Nakabayashi's mansion and got hired by Yoshitaka immediately, for Yoshitaka is not only a rich boy but also a pervert with uniform fetishes, who wants to be addressed as goshujin-sama (master). Having nowhere else to settle down along with Mitsuki's pet alligator Pochi, Izumi accepted the job reluctantly.
An art student named Jin Mikuriya carves a statue from the wood of the Kannagi tree only to have the statue come to life in the form of a goddess, who has now taken over the statue. He and "Nagi" work together to destroy the impurities that are gathering in the town.
Kinjirō Sakamachi has gynophobia (fear of women), due to his violent mother and sister. Subaru Konoe is the butler of his classmate, Kanade Suzutsuki, and has to dress as a male due to butlers having to be men. When Kinjirō discovers Subaru's secret, Kanade promises to cure Kinjirō of his phobia. Kinjirō and Subaru are forced due to circumstances to spend time together and defend Subaru's secret while trying to cure Kinjirō's fear.
Haruhi is a poor tomboyish student at a school for the ultra-wealthy, able to attend because of a scholarship, and unable to even afford a uniform. One day, she stumbles across the decidedly peculiar but very popular Ouran Host Club. She tries to leave, but accidentally breaks a vase, and unable to pay for it, she's told that she'll have to stay and do odd jobs. That is, until they decide she would be more valuable as a club member. Not realizing she's female due to her appearance, they fix her up and give her a male uniform. She's an instant hit, so they decide to have her keep up the charade even after they find out the truth. Haruhi, being average almost to a fault, doesn't know what to make of the unconventional activities of the Host Club (or of the even more unconventional members), but having little choice, she plays along. Before long, real bonds are formed, friends made, and Haruhi finds herself accepted in a way she could never have been otherwise in this affluent school.
Due to poor grades, Tsukune Aono, an average high school student, has been unable to get accepted into any private academy of his choice. By exceptional accident, the only school to accept him turns out to be anything but ordinary; the school is attended by youkai disguised as humans. Fearing for his life, he attempts to escape only to meet Moka Akashiya, a beautiful girl who just happens to be a vampire. Despite this, Tsukune decides to stay at the academy, hiding his human nature from students and teachers. Tsukune also discovers that when the rosary around Moka's neck is removed, her true nature emerges.
A new semester has arrived for Tsukune and the gang featuring a handfull of girl obsessed female first years and it seems like among these first years emerges another vampire who holds a grudge against her sister Moka. What shall this grudge lead to in the future and shall Tsukune suceed in taming this new problem child into his friend, no one knows what the future holds.