A 3rd world war seems to be looming on the horizon as somehow, the world all seems to be turning against Academy City thanks to the influence of the Roman Catholic Church. Touma Kamijou and Index are both sent to Avignon, France in order to help destroy an artifact being used by the Catholic Church to turn the world against the Science Side and cause war. However, they disappear soon upon arrival.. and Ben and Mikoto step in to search for them. Things get more difficult however when Vilgax makes a surprise visit to France.. and Ben finds himself facing another member of God's Right Seat, Terra of The Left, while Mikoto is left to fend against the mysterious Malware, a being born of Tree Diagram and the DNA of Upgrade. The world seems to be turning further upside-down as the occult, science, and what lies beyond our planet get mixed in a titanic showdown.