After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

Recap of episodes 1-13.

The story of the film is set after the conflict instigated by Toyotomi Hideyoshi ended, but not before the Battle of Sekigahara determines who shall be the Shogun of Japan.

(Source: ANN)

As the fall season nears its end, Chidori Yoshino, a member of Strega, abducts Junpei Iori. Meanwhile, Makoto Yuuki and the Specialized Extracurricular Execution Squad (SEES) annihilate the Arcana Hanged Man. Soon after, a mysterious playboy named Ryouji Mochizuki transfers into Gekkoukan High School's Class 2-F. Supposedly having achieved their goal, the members of SEES believe they are free from the battle that has ruthlessly stolen away the lives of their loved ones. And yet, Tartarus and the Dark Hour continue to exist, undeterred by the extermination of the twelfth Shadow. Distraught by their apparent failure, SEES must cope with their personal struggles and discover whose sake they fight for. As Makoto and Junpei's journeys of self-discovery progress, Ryouji's identity and the reason behind Aegis's hate for him become clear. [Written by MAL Rewrite]