Academy City is a highly developed place in terms of technology. It is said to be 20 to 30 years ahead of the rest of the world. Eighty percent of its 2.3 million residents are students. The focus of studies here is directed towards esper powers. Misaka Mikoto, one of the top level espers in town, shares a room with Kuroko Shirai, another high level esper who is a member of Judgement, a law enforcing agency composed of students. Both attend to Tokiwadai, a private school reserved for the high-leveled and the rich. Kuroko's partner at Judgement, Kazari Uiharu, is a low level esper who studies at Sakugawa middle school. Her best friend and classmate there is Ruiko Saten, a level zero (no esper powers). Together, the four encounter several adventures in the exciting scientific town.
Mikoto Misaka, one of the strongest Level 5 espers in Academy City, gave her DNA map to a certain doctor when she was young, believing that it may be used for greater good. Unfortunately for her, it ended up being used to create countless clones of herself; forming the Misaka network, in order to create the strongest esper by sacrificing these clones whom she considers as her own sisters.
Two years ago, Shibuya was ravaged by a biological terrorist attack using the deadly Ua virus. Maria Osawa was saved when her father inoculated her against the virus, but is left with partial amnesia from the shock. She works as a cameraman when she reunites with a girl named Canaan in Shanghai, China. A gifted assassin with synesthesia, she is under orders from an unknown organization for a yet unspecified mission.
Since ancient times, Japan has upheld the tradition of the 12 Zodiac signs. Eto-musumes (Zodiac girls), who have the appearance and behavior of the animals of the Zodiac, are pure hearted messengers who act as a bridge between humans and the gods. Every 60 years, the “ETM 12” tournament takes place in Tokyo’s Akihabara district, where aspiring girls from all over Japan gather for the chance to become the next zodiac sign.
The Japanese Ministry of Defense has an anti-paranormal special forces group called the Paranormal Disaster Countermeasure Headquarters. They're the ones responsible to protect Japanese soil and its people from supernatural and paranormal events. However, things didn't go so well in one of their missions, which leads to intervention by the Ministry of Enviroment's Supernatural Disaster Countermeasures Division after the PDCH has sustained large numbers of casualties battling demons.
Liones Yelistratova is the naive princess of a small nation, who goes to Hokkaido to enter ALCA, an educational institution dedicated to teaching Logicalists who uphold world peace. Liones enters Class S, and encounters many unique classmates, including Logicalist Nina Alexandrovna.
Guri is an angel with a mysterious item that turns any two people who kiss into a couple. She appears before a high school boy named Seiji Aino. However, there is a yandere high school girl named Akane who loves Seiji.
The relationship between Yuuta and Rikka starts to develop slowly in their own unique way as they begin to live together with Kuzuha under one roof. However, "chuunibyou"-plagued Satone, Yuuta's old acquaintance, showed up in the most unexpected place and time; challenging their budding, yet fragile relationship. Meanwhile, the rest of the Oriental Magick Napping Society in Summer club members continue to expand their own unique selves and relationships with one another.
Tokiha Mai and her sickly younger brother, Takumi, have received a scholarship to attend the prestigious Fuuka Academy. On the way, the ferry they are travelling on becomes the site of a destructive battle between two girls wielding apparently supernatural powers. This is only the beginning of their troubles, as Mai learns that she herself possesses these powers - the powers of a HiME.
Right after starting middle school, Akari Akaza joins the Amusement Club which is composed solely of her two childhood friends, Kyouko Toshinou and Yui Funami. Chinatsu Yoshikawa, Akaza's classmate, becomes a member after finding out about the dissolution of the Tea Club. The Amusement Club, situated at the tea room facility since the Tea Club disbanded, has no clear purpose, being free for the girls to do whatever they want.