In 1939, after the world has been devastated by an invasion of the "Neuroi"—alien war machines of unknown origin—humanity continues to struggle in an uneven fight. With no conventional arms able to pierce through the aliens' hardy armor, resistance forces spare no expense in their search for a way to level the playing field.

Eventually, the so-called "Striker Unit" is designed—a state-of-the-art device utilizing the innate magical powers of young girls and turning them into deadly weapons. The women who are now gathering from all around the world to fight for the survival of the human race are known as "Witches," with the 501st Joint Fighter Wing—the "Strike Witches"—standing at the forefront of the deadly conflict.

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!

Six months after the battle in Venezia, Minna, Gertrud, and Erica are stationed at Saint-Trond Base in Belgica, joined by Karlsland witch Heidemarie. Ursula, Erica's twin, delivers a 50mm cannon and Jet Striker Unit, with Gertrud chosen to test them—despite Erica's concerns from a previous mishap. Erica later tests a Twin Striker with Ursula, but her impatience causes failure, leading to harsh words that dishearten Ursula. When Minna and Gertrud are ambushed by splitting Neuroi, Gertrud tries using the 50mm cannon but is overwhelmed. Hearing Minna in danger, Erica takes the Jet Striker and cannon herself, struggling to control them until Ursula arrives to help. Together, the sisters save Minna and defeat the Neuroi.

Learning that island of Delos has been taken over by Neuroi, Charlotte E. Yeager and Francesca Lucchini are teamed up with Hanna-Justina Marseille and her partner Raisa Pöttgen to draw out the Neuroi hiding within it. Francesca, who has strong family ties with Delos, objects to their superior's plan to destroy the island, so they work out a new plan to have Hanna and Raisa draw out the Neuroi while Charlotte and Francesca drop bombs on it. When this plan ends up failing, Francesca tries to attack on but is inevitably forced to retreat. The next day, before the bombardment on the island is due to take place, Charlotte, unwilling to let Francesca down, decides to make use of an abandoned ship's winch to pull the Neuroi out of its hiding place, allowing it to be destroyed without any damage to the island. Afterwards, Francesca takes Charlotte and the others on a tour of Delos and its artifacts.

Lynne and Perrine, along with Amelie Planchard, come across a young boy named Julius, getting treatment for his little sister Rose. As the two children stay at Perrine's house, with Julius proving a lot for Perrine to handle, Julius expresses a hatred towards witches for not coming to his father's aid when he went to battle at Arnhem Bridge. After learning that Perrine and the others are witches, Julius sneaks aboard a shipment bound for Arnhem Bridge to retrieve some personal belongings. With her Strike Unit in repair, Perrine steps in to protect Julius from the Neuroi until Lynne backs her up, with Julius helping Perrine in return when she injures her leg, allowing both her and Lynne to defeat the Neuroi. Afterwards, Perrine takes in both Julius and Rose to give them an education while Lynne receives a letter from Yoshika.

Yoshika leaps back into action to save her friend's father, but her striker unit almost blows up on the tarmac!

When a Neuroi strikes at Europe's biggest supply port on the eve of humanity's counterattack, Yoshika must hold it off alone, without any weapons at all!

Yoshika's lost control of her magic… again! It's time for more training and more hard work if she wants to get it back!

Shirley's world record was just broken, and she's not happy about it. As Shirley and Lucchini attempt to beat the new world record, an unusual Neuroi threat swiftly approaches.

The girls take a detour to Nederland, to help a legendary flower bloom.

When Erica is shot down in enemy territory, Gertrud will do whatever it takes to get her back.

A mysterious idol causes all the witches' breasts to grow bigger and bigger, and the girls gradually fall victim one by one...

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Rocket attacks from the Neuroi nest in Berlin are threatening the base in Kiel. Only Mina has what it takes to stop them, but her magic power is fading…

Operation Southwind begins with a full-scale air assault on Berlin. When Yoshika is ordered to stay behind to conserve her magic, Shizuka steps up to try and fill the hole.

With Miyafuji's magic power disabled, humanity is forced to use its backup plan: the powerful Ratte tank. But can they win without their ultimate ace?

Yoshika is trapped inside the dome around Berlin, and the rest of the Witches are cut off. Can they get inside to save her in time?