Shuumatsu no Izetta is set in an alternate 1939, where Germania has already carved a path of destruction across Europe and now prepares to strike at Elystadt, a small alpine kingdom that seems certain to collapse under the weight of a far stronger army and a string of earlier victories. As the threat closes in, Princess Ortfiné "Finé" Fredericka von Eylstadt is seized by Germanian soldiers while en route to a crucial meeting with Britannia, leaving Elystadt with little hope of diplomatic rescue.
At the same time, a Germanian transport mission goes awry and frees Izetta, the last witch alive. When Izetta recognizes Finé from their shared childhood, she uses her magical power to save the princess and vows to defend Elystadt. What follows is a desperate wartime alliance between a frightened kingdom and the last surviving witch, as Finé and Izetta become the country's best chance to stand against an imperialist war giant and buy Elystadt one final opportunity to fight back and change the course of the conflict.