World War III, caused in Russia by Fiamma, the final member of the Roman Catholic Church's secret group God's Right Seat, was brought to an end thanks to the efforts of Kamijou Touma. However, he disappeared at the end of that war.
This is a world without that hero.
The magic side is being reorganized and improved, and days of rest have arrived for its believers.
In the headquarters of the science side, Academy City, Accelerator, the strongest Level 5, has cut his ties with the darkness and is now living a noisy but calm normal life with Last Order and Misaka Worst. Not a sign of Group remains.
With the material for negotiating with the darkness in hand, Hamazura Shiage, a former Skill-Out Level 0, has returned from Russia and formed a new Item with Kinuhata, Takitsubo, and the returned Mugino. They have begun their activities once more.
Those graduates of the darkness have obtained peace and quiet. That is, until the brutal Freshmen appear before them.