In 1939, the imperialist nation of Germania launched a sudden invasion of its neighboring countries. This conflagration engulfed all of Europe in one fell swoop, and the era was dragged into the maelstrom of war. Then in 1940, Germania set its sights on Elystadt, a tiny principality blessed with breathtaking greenery and water in the Alps. Izetta is a descendant of a clan of witches who had passed down mysterious powers for generations. Since she was little, she and her grandmother lived their lives on the road, traveling between European countries in order to hide these powers. Fiine is the sole daughter in line to succeed Rudolph III, the ruler of the Principality of Elystadt. Since her father has been stricken by illness, she has been busy preparing for Germania's invasion in his stead.
After discovering that Neuroi are capable of communication with humans and making peace with the nest above Gallia, the Witches squads are now on a mission to re-establish communication when the Neuroi completely vanish after a sudden attack. It is then that they discover a new massive nest that just appeared covering almost all of Europe. Ruthless and without mercy it annihilates allied forces along with many Witches. Word of the attack reaches Fuso and a support battalion is deployed to rescue the survivors. Among the rescue team is the former Striker captain Sakamoto Mio and the now civilian Miyafuji Yoshika who wants to save her dear friends.