Mikoto Misaka, aka Batgirl, continues to watch over Academy City, while receiving training from Batman on the side, continuing to grow in her path as a hero now that she can use her powers while under the bat's mantle. However, once more, dark forces move against our hero and her friends. A menacing figure known as the Arkham Knight, is bent on destroying Mikoto's mentor Batman. And he has a message for Batgirl, join him, or get taken down.. hard. And with Batgirl's refusal, comes a swift invasion of Academy City by the Knight's personal highly trained militia, and the Arkham Knight seeks now to obtain a certain magical set of Grimoires to use in his vengeance on Batman. Can Mikoto defeat the Arkham Knight? And just who is this strange man, who seems to know so much about her and Batman?

After the death of her parents, she couldn't take it anymore, living in Academy City. The darkness, the guilt that haunted her, it was too much. So Mikoto Misaka, Level 5 Esper, super powered Electromaster, left, going off to America to study in Gotham City. 1 year later, Mikoto returns to Academy City for unknown reasons, instantly seeking out all her old friends.. and reconnecting with everyone. However, at the same time, the Vigilante from Gotham City known as Batgirl is sighted in Academy City, destroying labs and infiltrating various organizations. Mikoto, who studied in Gotham for the duration of her time away, denies knowledge of what's happening.. however.. her friends begin to suspect that she might know more about this Batgirl, then meets the eye..