Yoshika Miyafuji is a fourteen-year-old girl who possesses magical powers that can heal. One day she is approached by Mio Sakamoto, Major of the 501st Joint Fighter Wing a.k.a. Strike Witches to join her team. A few days after Yoshika turns down the invitation because of her abhorrence toward wars, she receives a letter.

When Sakamoto's strike unit malfunctions, Yoshika is forced into a solo dogfight against a rapidly-regenerating Neuroi! The bombastic beauties of the 501st Joint Fighter Wing race to provide backup, but will they arrive in time?

Yoshika is permanently grounded after suddenly losing the ability to fly, but a prototype Striker Unit inspired by her father's letter may hold the key to putting her back in action!