As New Year’s Eve draws closer, preparations for a holiday party are underway in Petersburg. In anticipation of the event, Eila Ilmatar Juutilainen of the 501st Joint Fighter Wing is determined to take Sanya V. Litvyak on a leisurely walk around the city. However, despite Eila's best intentions, she gets interrupted every time she gets a chance to ask Sanya out, ruining the moment and separating the girls. To make things worse, a Neuroi is approaching the base, threatening both the squadmates and the celebration in Petersburg.

As humanity's war with the Neuroi—a mysterious, hostile alien race possessing weapons of unparalleled power—continues being fought across Europe and Africa, a new fighter squadron is formed. The 502nd Joint Fighter Wing, also known as the Brave Witches, operates on the eastern front, scouring the icy vastness of Orussia in search of alien invaders. However, one of the Brave Witches' members suffers severe injuries on her way to the squadron's headquarters, rendering her unable to participate in any operations. As a result, her sister, Hikari Karibuchi, volunteers to take her place. Though not possessing any special abilities or significant magical powers, she is determined to live up to the expectations of her new comrades and prove herself worthy of the name of a Witch.

Following the conclusion of the three-way organizational war, government bureaucrat Ango Sakaguchi recalls an event that transpired years ago, after the death of the former Port Mafia boss. Osamu Dazai, still a new recruit at the time, was tasked with investigating rumors related to a mysterious explosion that decimated part of the city years ago—and its connection to the alleged reappearance of the former boss. Due to circumstances out of his control, he is partnered with Chuuya Nakahara, the gifted yet impulsive leader of a rival clan known as the Sheep, to uncover the truth behind the case and shine a light on the myth of Arahabaki—the god of fire who might just lead Dazai to the case's solution. Meanwhile, in the present day, it is business as usual once again for the Armed Detective Agency. Their peaceful break will not last for long, however, as enemies old and new gather their strength and prepare for another face-off.

Despite their differences in position, three men—the youngest senior executive of the Port Mafia, Osamu Dazai; the lowest ranking member, Sakunosuke Oda; and the intelligence agent, Ango Sakaguchi—gather at the Lupin Bar at the end of the day to relax and take delight in the company of friends. However, one night, Ango disappears. A photograph taken at the bar is all that is left of the three together. Fast forward to the present, and Dazai is now a member of the Armed Detective Agency. The Guild, an American gifted organization, has entered the fray and is intent on taking the Agency's work permit. They must now divide their attention between the two groups, the Guild and the Port Mafia, who oppose their very existence.