Although he attends the Royal Magic Academy in the Kingdom of Wenias, Sable has the worst grades in the entire school. As he has no memories of his time before attending the institution, when Headmaster Albus tasks him with a special training regimen in the south, Sable eagerly accepts it. Alongside the Dawn Witch, Roux Cristasse; Holt, a human girl with antlers; and Kudd, a lizard Beastfallen, Sable must establish a village of witches in a region where anti-witch sentiment remains strong. During their journey, the quartet avoids former members of the Dia Ignis Arbiters—a group of witch hunters notorious for murdering witches and civilians alike. Five years ago, their organization was disbanded and given amnesty with the end of the war between the Church and witches, but their members still linger and are ready to capture any mages they come across. Thankfully, with Roux's Staff of Ludens, the witch-eater, and Sable's unlimited supply of magic, the group may be able to accomplish their mission for Albus. If not, Sable's memories of magic and the academy will be taken away, and he will be left with nothing to guide him to the silver-haired mage who first rescued him.

With the initiation of the Patrian civil war came the creation of half-beast, half-human soldiers—a development of the outnumbered Northerners in a desperate attempt to counter the overwhelming Southern forces. Able to quickly dominate battlefields and achieve victory with ease, the soldiers' godlike abilities earned them the name Incarnates. However, as the war raged on, the Incarnates encountered a problem involving the beasts inside them that they were unable to rectify by ordinary means. Once the war was over, mysteries and accounts of the Incarnates submitting to the misfortune of their war days surfaced. Aware of the horrors they faced during the war, Special Sergeant Major and former captain of the Incarnates Hank Henriette becomes a Beast Hunter—those who take the lives of Incarnates who have succumbed to the issues they experienced on the battlefields. After witnessing her father, a former Incarnate soldier, meet his end at the hands of one such Beast Hunter, Nancy Schaal Bancroft resolves to hunt the man who took her father's life. However, Nancy's eye-opening encounter with the Beast Hunter influences her to instead seek the reason behind her father's death and the Incarnates' problematic existence in society.

Recap of episodes 1-13.

​Shiki Ryougi, Mikiya Kokutou, and Touko Aozaki begin investigating a bomber after they witness a nearby explosion. That same night, Shiki catches a glimpse of the bomber, and as a result, he becomes fixated on her. To get rid of her, the madman plays a game of cat and mouse in attempts to lure her to an empty parking garage. And bombs are not the only thing he has in his arsenal: he also possesses the ability to see the future, and he intends to bring an end to Shiki. Elsewhere a few days prior, a student at Reien Girls' Academy, Shizune Seo, plans to head home for the summer. However, while exiting a bus, she has a vision of the future involving a nearby stranger's death. While trying to warn the stranger, she meets Mikiya—who succeeds in utilizing Shizune's information effectively. Subsequently, an employee is sent on a job with his employer's 10-year-old daughter in tow. However, the subject of his investigation turns out to be a ghost from both of their pasts. Mirai Fukuin tells the stories set during the main timeline of the Kara no Kyoukai films, as well as one set in the future.