Eleven years after the introduction of internet-connected, augmented reality eyeglasses and visors, Yoko Okonogi moves with her family to Daikoku City, the technological center of the emerging half-virtual world. Yoko joins her grandmother's "investigation agency" comprised of children equipped with virtual tools and powerful metatags. She quickly crosses paths with Yoko Amasawa, an expert hacker of the virtual environment, as Amasawa relentlessly seeks to "unlock" the mystery of a computer virus that emerges from an inaccessible corrupted space.
Medaka Kurokami, a first year student at Hakoniwa Academy, excels at everything she does. She becomes the Student council president and along with her childhood friend, Zenkichi Hitoyoshi, she plans to solve all of the student body's problems that are submitted to a suggestion box, dubbed the "Medaka Box."
After Medaka Kurokami defeated Myouri Unzen (the head of the disciplinary committee), she is recruited by the headmaster to join the "13 Party" - an elite and select group of 13 Abnormal students from Class 13. Medaka discovers that they are taking part in the Flask Plan, which aims to create perfect humans by sacrificing all the students in the school. It is up to Medaka and the rest of the student council to stop it.