On a day when the space elevator "Endymion," constructed by Academy City, is nearing completion, Kamijou Touma and Index encounter a Level 0 esper girl named Misaka Shokuhou. Index and Shokuhou quickly bond over their "voracious appetite," a mysterious connection, and just as the three are enjoying their pleasant after-school time, Stiyl Magnus, accompanied by magicians, suddenly launches an attack. The target of this assault is none other than Shokuhou. Why would Shokuhou, a resident of the scientific world, be pursued by those from the magical world? Faced with the intense offensive from the magical world, Shutaura, representing Academy City, mobilizes the order maintenance forces to take action. Kamijou, Index, and Shokuhou find themselves thrown into chaos and confusion by this situation. Stiyl tells them, "The girl there will trigger a war between the magical world and the scientific world." As science and magic intersect, a story set on the stage of "Endymion" begins!