| ShortSummary | - Mio trains to obtain the true Reppuzan, and refuses to teach it to Yoshika despite her requests. Later, during a practice session with Perrine, Yoshika starts to have some trouble flying. Mysteriously, though, Yoshika is given a clean bill of health, and her Striker Unit is in perfect running condition. The next day, Yoshika and Lynnette are sent to the battleship Yamato to heal crew members injured in a lab explosion. When the Yamato and its battle group is attacked by a blimp-shaped Neuroi ship, Yoshika is unable to fly, leaving Lynette alone to defend the battle fleet while they retreat. As Yoshika laments her inability to help, she hears her father's voice and is presented with a new Striker Unit, which was developed based on his research findings. Now able to use her powers to the maximum with a Striker Unit built just for her, Yoshika manages to save Lynette just in time and defeat the Neuroi single-handedly. Later it was revealed that Yoshika's flight troubles are traced to her old Striker Unit's inability to withstand Yoshika's increasing power.
- Despite using up all her energy and passing out, Yoshika continues to use her healing abilities on Mio, eventually getting her into a stable condition. After Mio wakes up, Minna confines Yoshika to her quarters, refusing to hear her side of the story. Determined to find out the truth, Yoshika sneaks out and follows the Neuroi to its hive. There, Yoshika is shown the history of the Neuroi, as well as some scientists utilising one of the Neuroi cores. Before Yoshika can learn more, a strange mech utilising similar technology appears and destroys the Neuroi. Upon returning to base, the witches find themselves surrounded by military soldiers.
- When a suspicious new Neuroi is spotted in the clouds, Yoshika is assigned on night patrol with Sanya Litvyak and Eila Juutilainen to investigate. During one of their missions, the Neuroi appears again, targeting Sanya, but the three work together to destroy it. As Yoshika and Sanya share the same birthday, they hear Sanya's father play a song for her over the radio.
- As the Neuroi continues to attack the plane, a fleet of battleships provide support, but are easily defeated by the Neuroi. With Mio still unable to use her shield, Yoshika flies into battle to protect the ships with her enhanced magic. Mio then uses her enhanced katana to slice through the Neuroi's beam and destroy it. However, it soon reforms itself, its core continuously shifting places to avoid being destroyed. Yoshika has a tough time facing it until Shirley, Lucchini, Lynette and all the other Witches arrive to assist, giving Mio the opportunity to destroy it with her katana. Setting up base in Romagna, Minna officially reforms the 501st Joint Fighter Wing.
- The military, led by General Trevor Maloney, overthrow the base and disband the Strike Witches, instead opting to use their mech, the Warlock, which Yoshika recognises from the visions the Neuroi showed her. The witches are left with no choice but to return to their home countries. However, Minna, Barkhorn and Erica decide to stay behind to uncover the truth. When the Warlock attacks a Neuroi nest, it turns black and turns against Maloney, attacking everything in sight. With Yoshika, Mio and Perrine aboard the Akagi as it is attacked, Mio reveals a hidden Striker Unit which Yoshika offers to fly.
- Worried about Mio's strength, Minna tries to convince her to stop going into battles but fails. After Barkhorn visits her awakened sister, she finds a letter addressed to Minna, warning her not to delve in any further. Meanwhile, Perrine's jealousy over Yoshika reaches its peak and she challenges her to an ariel duel, which is soon interrupted by work of a Neuroi. When Yoshika confronts the Neuroi, it turns into a human shape and appears to communicate with her. When Mio arrives and Yoshika tries to defend it, it attacks Mio and pierces through her shield, dealing critical damage.
- The Witches discover a huge Neuroi spire whose core is in a location far beyond the altitude that their Striker Units can reach. Formulating a plan using rocket boosters in stages to reach the required altitude, Sanya is chosen to attack the core. Having never needed to use a shield in combat, Eila becomes furious when Yoshika is chosen to protect Sanya instead of her. Eila tries to get Perrine to train her to use shields, but to no avail. Sanya becomes annoyed with Eila's willingness to give up and gets into a fight with her. The next day, as the Witches launch Sanya and Yoshika to the stratosphere, Eila apologizes and expresses her desire to protect Sanya. Seeing this, Yoshika decides to switch places with her. Eila finally uses her shield to protect Sanya as she destroys the core.
- Mio still experiences power drains from her use of the true Reppuzan. Later, she scolds Yoshika for touching her sword--which reacted to her powers and nearly caused her to faint. Later, Mio and Minna receive orders from their superiors for a final attack on the Neuroi nest. They plan to defeat it by powering the Yamato with Neuroi technology. The mission's failure would mean the surrender of Romagna and the disbanding of the 501st Strike Witches. Mio becomes determined to complete the True Reppuzan, but Minna, aware that her sword has drained nearly all of her magical power, stops her--which Yoshika overhears. The next day, they begin the charge and Mio's Reppuzan fails to work, much to her despair. Meanwhile, the Yamato activates its Neuroi Dynamo, allowing it to fly and repair itself. But when the Neuroified Yamato hits the hive bow first, its Neuroi Dynamo stopped working, paralyzing its firing controls. With the mission deemed a failure, Mio, never giving up, charges towards the Yamato to attempt to restart the Dynamo with her remaining magic power.
- Yoshika finds it odd that Commander Minna-Dietlinde Wilcke has prohibited the men from the hangar from talking to Strike Witches. The Akagi comes to visit to thank Yoshika for her help during the Neuroi attack. One of the crew tries to give Yoshika a thank you letter but is stopped by Minna. The next day, the witches go up against a dividing Neuroi, and Minna notices a weakness in Mio's shield. Following the battle, Minna checks the site, where she finds a memento from her old boyfriend who died in the war. As the Akagi leave on their next mission, Yoshika sends them off and Minna sings them a farewell song. However, later that night, Minna points a gun at Mio.
- While Yoshika, Shirley and Lucchini is in Romagna's capital, Roma, buying supplies and gifts, Lucchini spots a girl named Maria being accosted by some suited men and rescues her. The two quickly become friends and spend the day exploring the city, although Lucchini ends up spending all the food money Shirley gave her. When a Neuroi ship appears, Lucchini rejoins Yoshika and Shirley to defeat it. Afterward, Lucchini treats Maria to a bird's eye view of Roma, telling her the importance of protecting it. After they return home, it is revealed that Maria is actually the Duchess of the Principality of Romagna, who gives her thanks to Lucchini during her inauguration by airdropping food supplies to the Witches.
- On the day of her commendation, Erica Hartmann misplaces her panties, so she steals Lucchini's. Lucchini in turn takes Perrine's panties, but soon gets spotted by the others and runs away, taking Yoshika's underwear with her. As Lucchini continues her escape, she also takes Eila's tights, which causes Eila to borrow Sanya's. Whilst hiding, Lucchini accidentally switches the Neuroi alert on which causes confusion among the troops until Erica busts her. As Lucchini is forced to sit panty-less through Erica's ceremony, a breezy wind reveals the true culprit.
- After enjoying the newly-installed bath, a strange bug that Lucchini found earlier in the morning is embarrassing the Witches by literally getting into their pants, as well as causing electrical outages around the base. They soon realize that the bug is the core of a Neuroi ship that is sapping electricity from the base, disabling the alarm system, as it feeds a larger unit lurking near the base. After the Witches ensue a lengthy chase for the bug around the base, it is Minna who inadvertently destroys the Neuroi bug when it crawled inside her pants, destroying the larger unit as well. It is technically Minna's 200th Neuroi kill, and she was awarded a medal by the Luftwaffe for the milestone.
- Mio progresses in perfecting the true Reppuzan, but it drains much power from her. After Minna proposes an operation to attack a Neuroi base, the top brass send in Captain Hanna Marseille of the 31st Karlsland Luftwaffe Storm Witches to join the mission. Since Barkhorn and Hanna don't get along, Erica volunteers to accompany her on the mission. After fooling around in a training session, Hanna and Erica are ordered to stay in a room together to learn to cooperate. Hanna is obsessed with winning, and has always wanted to settle things with Erica, whom she views as her equal, but as of late she is annoyed with Erica's lack of competitive spirit. But when Hanna badmouths Barkhorn, who wanted an autograph for her sister, Erica agrees to compete with her during the mission. When they reached a draw after destroying the Neuroi, they have a tiebreaker dogfight, also ending in a draw. Before she leaves, Hanna decides to give the autograph.
- Mio meets up with Junko Takei of the 504th Joint Fighter Wing to learn about the new breed of Neuroi. Having gotten out of shape following inactivity during the past six months, Yoshika, Lynne and Perrine are sent to an old lady named Anna Ferrara, who teaches them the basics, namely how to ride old fashioned brooms. They struggle at first, but they soon start to get the hang of it. During their training, a Neuroi ship threatens to come into contact with Anna's home, but the girls team up to defeat it.
- The Witches obtain a prototype Jet Striker model from Karlsland. After an argument between Shirley and Barkhorn, Barkhorn gets to use it, as Lucchini convinces Shirley not to use it after trying it herself. Barkhorn relishes in the Jet Striker's power and outperforms Shirley in a series of performance tests, but it ends up draining too much of her magic, causing her to faint midflight. Minna prohibits anyone from using the Striker as a result, and confines Barkhorn to her quarters. She breaks the ban anyway when a fast Neuroi appears. Although she defeats the Neuroi, Barkhorn faints as, this time, the Jet Striker goes out of control, forcing Shirley to push her Striker Unit to its limits to save her, destroying the prototype in the process. Later, Erica's twin sister, Ursula, pays them a visit, with a shipment of potatoes as a token of apology for the flawed prototype.
- Despite Minna's objection, Mio heads inside the Yamato and gives the Neuroi Dynamo her remaining magic power, allowing the cannons to be fired, which destroys the Neuroi nest. It is not enough, however, as the Neuroi somehow regenerates, trapping Mio in its massive core, and using her shield. Not giving up, Yoshika, with backup from the other Witches, retrieves the Reppumaru and destroys the giant Neuroi core with a Reppuzan that drained all of her magic power, freeing Mio in the process. With Venezia finally free from the Neuroi, the 501st Strike Witches are once again formally disbanded; and Yoshika begins her medical career.
- The Witches head to the Britannian coast for a mix of training and relaxation while Charlotte 'Shirley' Yaeger tunes up her Striker Unit, chasing her dream to break the sound barrier with it. Whilst messing around, Shirley's friend Francesca Lucchini accidentally damages Shirley's Striker Unit and hastily puts it back together. When Shirley uses this unit during a surprise Neuroi attack, she is able to break past Mach 1 and destroy the enemy.
- Luftwaffe ace Gertrud Barkhorn is distracted by the state of her seriously injured younger sister and becomes cold towards Yoshika, who bears a resemblance to her. Yoshika is also berated by Perrine Closterman, who is jealous of her familiarity with Mio. When a Neuroi threatens Barkhorn's home country, she tries to handle everything herself and gets critically injured. Although Barkhorn insists she be left to die, Yoshika heals her, telling her she should protect as many people as she can. With this resolve, Barkhorn recovers and defeats the Neuroi, and later decides to go visit her sister.
- With reinforcements a long way away, Mio along with the ship's airforces fight against the Neuroi ship. Yoshika, frustrated that she can't do more to help, decides to don a Striker Unit, a device used to make witches fly, to assist Mio. Although she is hesitant in using a gun, she manages to do enough to allow the reinforcements to defeat the Neuroi. After finding that her father is still dead, Yoshika decides to join the Strike Witches so she can help people.
- Yoshika is introduced to the other members of the 501st Joint Fighter Wing. The former newest Witch, Lynette Bishop, is distressed that Yoshika's apparent talent surpasses her own, since she lacks confidence during battle. When a decoy leaves Yoshika and Lynette as the only defense against a Neuroi attack, Yoshika helps to stabilise Lynette so she can defeat the Neuroi herself.
- While visiting Gallia, Perrine learns that children can't get to school because the bridge is broken. This preoccupies her, even thinking of selling the last family heirloom to fund the bridge's repairs. On a training trip at the beach, Lucchini finds a treasure chest, which Perrine salvages in the hope of finding treasure. After going through an endless number of chests, they find a puzzle chest containing a map, which Perrine, Yoshika, Lynnette and Lucchini follow to an underwater cave filled with booby traps. Meanwhile, while looking for them, Mio and the others encounter a trap which causes Mio to become drunk, kissing Minna and running off. Perrine's group comes across a room with a statue which Perrine defeats when it attacks them. They eventually find the treasure, which is nothing more than a herb and spice garden. However, a slightly hungover Mio reassures Perrine that it's the feelings that people truly treasure. After returning to base, Perrine receives a letter from Gallia informing her that the children worked together to build a new bridge.
- Yoshika goes into battle against the Warlock. After Minna's group apprehends Maloney, they use Barkhorn's strength to retrieve everyone's Striker Units so they can assist Yoshika in taking down the Warlock. However, it assimilates with the Akagi, turning it into a giant airship. Whilst everyone else provides cover, Yoshika, Lynne and Perrine infiltrate the ship, and use Yoshika's Striker Units to destroy the core. With the Warlock defeated, the Nueroi nest over Gallia disappears, and the 501st Joint Fighter Wing officially disbands. However, six months later...
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