​Like many in her class, Koyuki Honda looks forward to her graduation ceremony. However, while her peers have family to attend, Koyuki has no one, as her only family—her brother—died years ago. While visiting his grave, she meets two brothers named Kiri and Victor Putin chasing a strange creature. They try to assure her that they are just actors shooting a movie; Victor, however, piques Koyuki's curiosity about the old legend of the clock tower at the cemetery: if you make a wish under the clock tower at midnight during a full moon, time will turn back, allowing someone to reclaim what they have lost. Deciding to make her wish, Koyuki learns the horrifying truth: the legend is a ruse for time demons called Horologues to steal humans' time. As they are drawn to regrets, Victor uses Koyuki as bait to lure a demon there. Kiri and Victor explain that they are Chronos Rulers, warriors who fight against the Horologues using the Oath of Time—an item allowing them to speed up or slow down time. With the demon destroyed and the crisis averted, Koyuki is able to go on her way free from regrets. However, she is not the only human with sorrows. The two boys must continue to hunt down Horologues in order to keep humanity safe.

As another school year begins drawing to a close, the third-year high school students move steadily toward the next milestone of their lives: graduation. Among them are Mio Natsume, a girl burdened with lingering feelings; Hazuki Morikawa, a member of the concert band but distant from the others; and Haruto Souma, an athlete obsessed with baseball. Meanwhile, second-year student Ena Komiya seeks to revive the photography club to its former glory, refusing to let the organization be disbanded. Though this group lacks a strong connection with one another, their lives suddenly cross paths with the arrival of a third-year transfer student. While a transfer so close to graduation is unusual for most, it is business as usual for Eita Izumi. Due to his father's work, he has never been able to stay in one place for very long. But as luck would have it, their most recent relocation has returned Eita to his hometown for his final semester of high school. For better or worse, it also sparks the rekindling of old relationships left behind in the past. With graduation already causing its own share of anxieties, Eita's sudden arrival brings these students' carefree days to an abrupt end. Long-forgotten memories, deeply buried emotions, and inspiring new passions—everything is brought to light in their bittersweet final semester.

Naoya Mukai is having the time of his life after his childhood friend Saki Saki finally accepts one of his countless confessions. Ensuring that their relationship will stay strong, he spares no effort in showering affection to his now beloved girlfriend. However, one afternoon, another girl named Nagisa Minase suddenly confesses to Naoya following months of preparation. Even though he politely rejects her, Nagisa's irresistible charm and determination continue to attract Naoya. Wanting to fulfill both Saki and Nagisa's desires, Naoya ends up proposing a crazy idea—to date the two of them simultaneously, with both girls fully aware. This unprecedented state of affairs ultimately causes wacky and hilarious situations in whatever they do to keep their unusual relationship going.

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.