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.

On their journey to Britannia, Yoshika and the others are assaulted by mysterious invaders called the Neuroi, menacing beings from another world. In order to buy time until reinforcements arrive, Major Sakamoto sallies forth alone, only to be met by a fierce attack from the opposition. Despite her best efforts she is driven back and ultimately cornered. Yoshika can do nothing but wait in terror inside the battleship.

Yoshika makes her decision to join the Strike Witches. Lynette Bishop, another rookie witch who is 15 years old, shows Yoshika around. Although Yoshika is nervous about her new assignment and understands nothing about the arrangement of the troop, Lynette acts in a somewhat unfriendly manner, adding to Yoshika's anxiety.