To Aru Majutsu no Kinsho Mokuroku - Road to Endymion

Set in a city of not only scientifically advanced superhuman students, but in a world where magic is also real. Kamijyo Touma's right hand, the Imagine Breaker, will negate all magic, psychic, or divine powers, as well as his own luck. One day he finds a young girl hanging on his balcony railing. She turns out to be a nun from the Church of England, and her mind has been implanted with the Index Librorum Prohibitorum—all the magical texts the Church has removed from circulation. (Source: Wikipedia) *Note: Includes 16 prologues, 18 epilogues, and 6 extras.*

Just before the completion of the Academy City space elevator "Endymion", the main characters Kamijou Touma and Index encounter a level 0 girl named Arisa. The Magicians are after Arisa, and they attack Academy City. A female leader named Shattoaura leads a unit from Academy City against the attack. Kamijou and Index learn from Stiyl that Arisa is key to a brewing war between the sides of Magic and Science. When science and magic cross paths, the story begins with Endymion as its stage!