As Christmas Eve approaches Academy City, an array of decorative festivities adorn the streets. While the rest of the city is getting into the merry mood, it seems gloom is all that Touma Kamijou experiences. After suffering from one misfortune after another, he encounters Mikoto Misaka escaping from the watchful eyes of Tokiwadai Middle School in an attempt to enjoy the Christmas atmosphere. The two agree on making the most out of this dreadful holiday; however, unbeknownst to them, a mysterious third party observes their every move.

Elsewhere, the newly instated Academy City Board Chairman initiates his first operation—a plan that will turn the entire city's framework upside down. Naturally, as he seeks to leave every stone unturned, previously hidden enemies begin to reveal themselves along with their malicious intents...