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Set in a world where science clarifies supernatural powers. In a huge college that has power development in its curriculum.

The second season of Toaru Majutsu no Index. Index is still a fugitive and many powerful magical organizations and individuals want to take her to use the books in her memory, eliminating her in the process.

Academy City is a highly developed place in terms of technology. It is said to be 20 to 30 years ahead of the rest of the world.

In the movie's story, just before the completion of the Academy City space elevator "Endymion", the main characters Kamijou and Index encounter a level 0 girl named Arisa. The Magicians are after Arisa, and they attack Academy City.

After the unsustainable growth of the human population on Earth, the United Nations has opted to colonize Mars. During this expedition, the humans discovered two alien technologies: The Bacillus virus and the Crusnik nanomachines.

The second season will focus on The Sisters Arc. Lasting only a single volume in the Toaru Majutsu no Index light novels, it was later expanded greatly in the Toaru Kagaku no Railgun manga.