"Strike Witches" is set in an alternate version of Earth during the 1940s, where humanity faces an alien threat known as the Neuroi. These mysterious beings, resembling mechanical insects, have invaded and occupied large portions of the world, rendering entire regions uninhabitable. To combat this menace, humanity develops advanced technology that combines magic and machinery, enabling certain individuals to wield powerful weapons and flight capabilities. These individuals, known as Witches, are young girls who possess magical abilities and are equipped with Striker Units—mechanical devices attached to their legs that allow them to fly and fight.

The story centers on Yoshika Miyafuji, a kind-hearted and skilled healer from Fuso (a fictionalized version of Japan), who is recruited into the 501st Joint Fighter Wing, an elite unit of Witches tasked with defending humanity against the Neuroi. The 501st, also known as the Strike Witches, is composed of girls from various nations, each representing a different country and bringing unique abilities to the team. Key members include Mio Sakamoto, the stern and experienced leader; Lynette Bishop, a sharpshooter from Britannia; and Perrine H. Clostermann, a proud and disciplined Witch from Gallia.

As the series progresses, the Strike Witches engage in numerous battles against the Neuroi, uncovering the aliens' weaknesses and developing new strategies to counter their evolving tactics. The narrative explores the personal struggles and camaraderie of the team, highlighting their growth as individuals and as a unit. Yoshika, in particular, grapples with her role as a healer in a combat-focused team, striving to reconcile her pacifist tendencies with the necessity of fighting to protect others.

The series blends action, drama, and lighthearted moments, with a focus on the relationships between the characters and their shared mission. Themes of sacrifice, resilience, and unity are prevalent as the Witches face increasingly dire threats, culminating in a climactic confrontation with the Neuroi that tests their resolve and teamwork. The story also delves into the origins of the Neuroi and the true nature of their invasion, adding layers of mystery and intrigue to the overarching plot.