The story is set in a world where supernatural powers exist through science, and magic exists through religion."Academy City." 2.3 million inhabitants. 80% of the students are active in the "Brain Development Program" and out of those only 7 are Level 5s.Meet the civilian protagonist Mikoto and her friend Kuroko, maintainers of peace and order at the University district, as members of the 'Judgment'.

The manga focuses on a certain unnamed character who appears throughout the story of A Certain Scientific Railgun and A Certain Magical Index, and whose name is revealed in this story set at Tokiwadai Middle School.