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.
Lain Iwakura appears to be an ordinary girl, with almost no experience with computers. Yet the sudden suicide of a schoolmate, and a number of strange occurrences, conspire to pull Lain into the world of the Wired, where she gradually learns that nothing is what it seems to be... not even Lain herself.