Having lasted merely two weeks, World War III has come to an end. Both Accelerator and Hamazura Shiage have returned home to the people they cherish most after overcoming their individual conflicts. The world is at peace and Academy City continues on as normal while the magicians focus their efforts on repairing the damage they took from the war.

Among this tranquility, however, someone is missing. Someone who used his right hand to save a young girl while changing the tides of war along the way: the "Imagine Breaker," Touma Kamijou. However, the disappearance of the self-proclaimed ordinary high school student has not affected the majority of the world as the temporary peace is soon broken when new threats, both espers and magicians, emerge across the globe. Now, the heroes of World War III must step forth into battle once more, facing off against some of the most powerful enemies imaginable in order to protect the people they hold most dear.