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. Since ancient times, humanity has been in conflict against an otherworldly enemy called "Neuroi". At the forefront of this war are teenage girls who can use magic, called "Witches", whose powers are enhanced via the use of equipment called "Striker Units".The year is now 1945, and the 501st Joint Fighter Wing, commonly known as the Strike Witches, have just successfully defended Gallia and Romagna from Neuroi depredations. With their immediate duty complete, the 501st is disbanded, and its member witches return to their respective countries.One of these witches is Miyafuji Yoshika who had lost her magic powers in the battle for Romagna. Still determined to do what she can to help others, she returns to her homeland of Fusou and studies medicine.During this time, she is visited by Fusou Naval Cadet Hattori Shizuka who offers Yoshika the opportunity to study in Europe. Yoshika readily agrees and, together with Shizuka, departs for Europe from Yokosuka.However, unknown to her, the Neuroi are once again on the move...