Touma Kamijou has vanished from Academy City, and the war that followed God's Right Seat's schemes is over. Accelerator has cut ties with the city's underground and settles into an uneasy ordinary life alongside Last Order and Misaka Worst, while Shiage Hamazura returns from Russia and pulls a reformed Item back together. The quiet does not hold: a group calling themselves the Freshmen arrives, and the magic-versus-science conflict around Index and Mikoto Misaka opens on a new front.