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.

Yoshika's plans to become a doctor are put on hold after a mysterious letter from her father leads to a reunion with Sakamoto. Elsewhere, her former Strike Witch comrades take to the air to battle a new breed of Neuroi!

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, Lynne, and Perrine report to a mysterious old woman for some special training, but their broomstick lessons are soon interrupted by a deadly Neuroi attack!

Barkhorn runs into big trouble during a test flight of the new jet striker unit, and only an extremely well-endowed comrade has the power to save her from the ultimate crash-landing!

A Strike Witch shopping trip goes up in flames when Lucchini spends the squadron's money on a sightseeing adventure and the town is attacked by Neuroi!

A menacing new breed of Neuroi looms high above the clouds, and the Strike Witches must equip themselves with experimental rocket boosters in order to reach the unprecedented altitude required to destroy their enemy!

Bath time is interrupted by an invasive insect hopping from one set of skimpy skivvies to another. The Strike Witches are up in arms over this shocking breach of their britches, and they'll do whatever it takes to protect their panties!

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!

When the girls of the 501st hit the beach for some special training, Lucchini discovers a treasure chest that leads to a treasure map that leads to booby traps!

Hartmann teams up with a famous witch on loan from another unit in order to defeat a special Neuroi that's impervious to airborne attacks! The new girl has lethal skills - and an attitude to match!

As the Strike Witches prepare for their most dangerous mission yet, Major Sakamoto - the bravest warrior among their ranks - can no longer hide the fact that her magic is rapidly fading!

Major Sakamoto risks her life to save the world, but the Neuroi hive proves nearly impossible to destroy. The witches are all out of magic, but Yoshika refuses to give up the fight!