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

Yoshika gradually orients herself to life as a member of Strike Witches. However, she is condemned by her supervisor Gertrud Barkhorn as being inexperienced. Desperate to win her acceptance, Yoshika gets carried away in her training when she suddenly comes face to face with Neuroi.

Shirley the speed freak is obsessed with trying to exceed sonic speed. Busybody Francesca Luccini meddles with the adjustments of Shirley's Striker Unit before the water training drill required by all members, which subsequently leads to an unexpected incident.

Yoshika and her comrades are attacked by the Neurois on their way back from a mission in London, but gets help from Sanya who happened to be on a night patrol. As a result, Yoshika is given orders to serve the night shift, and must spend the night in the same room with Sanya, when an envious Eila barges in.

Erica misplaces a key part of her uniform (panties), causing a chaotic incident in Witches Base.

Commander Minna begins to act strangely when the crew of the newly-repaired Akagi shower Yoshika with praise for her heroic action.

Perrine's jealousy reaches the peak, and she challenges Yoshika to an aerial duel. Their bout is cut short by a surprise Neuroi attack, and a weakened Mio scrambles to aid them despite Minna's protests.

Despite her efforts to heal Mio's grievous wound, Yoshika is confined to her quarters. With the other Witches doubting her story of the human-form Neuroi, Yoshika takes off by herself to find the truth.

The 501st Joint Fighter Wing is disbanded with the unveiling of the unmanned anti-Neuroi unit, Warlock. As the Witches scatter, something goes very wrong during the Warlock's sortie against the nearby Neuroi hive.

Yoshika launches alone against the out-of-control Warlock, desperately holding out as the other Witches race to join her and put an end to the monstrous hybrid of human and Neuroi technology.