Yoshika Miyafuji spends her days peacefully after returning to her hometown. Her former superior officer Mio Sakamoto and others arranged for Yoshika to study abroad at a medical school in Europe. Yoshika returns to Europe with Shizuka Hattori, who was Sakamoto's student at the naval academy. As Yoshika returns to Europe and new signs of Neuroi emerge, the other former members of the 501st Joint Fighter Wing, who were scattered in various locations, also begin to gather again. A powerful Neuroi then appears before Yoshika and Shizuka. (Source: ANN)

Six months have passed since the victorious Battle of Britannia and the reclamation of Gallia from Neuroi invaders. Yoshika Miyafuji, member of the famed 501st Joint Fighter Wing, has come back home to Fuso and graduated from middle school. However, her fight is far from over. She receives a letter supposedly sent by her long-deceased father, containing blueprints of a state-of-the-art Striker Unit he had been working on before his death. The Unit, designed specifically for Yoshika, might be capable of harnessing her extraordinary magical powers. Meanwhile, a new threat in Europe is rising. A Neuroi nest of an unprecedented size and might has appeared over Venezia, wiping out local Witch forces and instantly swallowing the northern part of the country. To make matters worse, a newly spotted humanoid type of Neuroi is attempting to come into contact with humans. Yoshika, incapable of abandoning her friends on the front lines, must once again venture to the war-torn continent.

In order to keep ocean peace, PKN was organized. It consisted of the state-of-the-art battle ships of various countries. However, they were raided during the foundation ceremony by the unidentified organization, USR, which plotted to conquer the world. They couldn’t be much for the submarine UX which was operated by Admiral Red of USR. But an old Japanese submarine, the 707 saved them, which was operated Captain Hayami at the risk of his life. One year later, succeeding to the 707, which had been ruined during the former fight, newly developed submarine, the 707 II, went for a sail. Among the crews, there were boys, such as Kenji, Goro, and Senta, who had been trainees. PKN formed a fleet led by the Great Guardian, which was the latest battle ship of the United States. However, the attacks of Submarine U were very server, and the fleet was defeated. Then, the 707 arrived. As soon as Red noticed the 707, he was glad to reunion with his rival and began to fight. Escaping from the submarine attack, they hid the 707 in the valley. But Red tried to destroy the valley in order to put the 707 into the torrents of mud. The 707 nearly escaped from it and got in the crater. However it was the pure water layer where the submarine couldn’t float up. At the moment, numerous torpedoes launched to the 707. (Source: AnimeNfo)

In the year 1939, humanity was on the verge of destruction. Equipped with weapons of devastating power, a mysterious alien race, known as the Neuroi, began an invasion of the Earth, ravaging the planet, obliterating countries, and vanquishing human armies. To counter this seemingly unstoppable force, the world's powers united. A new device was produced, called the Striker Unit, capable of facing Neuroi technology. Girls equipped with the Striker Unit became known as the Witches, forming humanity's last line of defense. They began their fight against the Neuroi, utilizing their now-enhanced magical abilities, flaunting destructive weapons no human could manage. Fast forward to 1944—Yoshika Miyafuji is a young teenage girl who eventually decides to join the 501st Joint Fighter Wing, known as the Strike Witches. With no formal training however, can Miyafuji learn to cooperate with her fellow Strike Witches? And if so, can she save humanity from the Neuroi onslaught?