Having won the 63rd National Sensha-dou tournament, the girls from Ooarai Girls Academy managed to prevent their school from closure by the Japanese Ministry of Education. However, new troubles loom on the horizon: a ministry official argues that the deal was not legally binding and that the Ooarai school carrier is to be decommissioned. Students and their families are frustrated with this injustice and overwhelmed with despair; it seems little can be done to save the school. Their last glimmer of hope is a proposed match against the All-Stars University Sensha-dou team, consisting of the most talented students from all over the country. Despite Ooarai being severely outnumbered and clearly outclassed, they accept the challenge.

The siblings Kashou and Shigure Minazuki enjoy the company of six catgirls. Chocola and Vanilla assist Kashou in his job as a baker at the patisserie La Soleil, while the others—Coconut, Azuki, Cinnamon, and Maple—accompany Shigure in her daily life back at their home. One afternoon, when Chocola goes out for an errand, she notices a green-haired kitten alone by herself at a park and decides to bring her back to the patisserie. Soon after, the Minazuki household adopts her and gives her a name: Cacao. With a new member in their family, the members of the Minazuki household continue their everyday lives—bound to become livelier than ever.

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?

In a research facility hidden away on a remote island, genius programmer Shiki Magata has lived as a recluse for years. She rarely sees guests, but associate professor Souhei Saikawa and university student Moe Nishinosono still seek her out. However, their meeting is cut short when they are caught up in a locked-room murder mystery. Everything is not as it seems, and many secrets are hidden. Within an isolated facility, a seemingly impossible and gruesome crime takes place, and Saikawa and Moe must unravel the truth behind the murder and Magata's shrouded past.