High school freshman Houtarou Oreki has but one goal: to lead a gray life while conserving as much energy as he can. Unfortunately, his peaceful days come to an end when his older sister, Tomoe, forces him to save the memberless Classics Club from disbandment. Luckily, Oreki's predicament seems to be over when he heads to the clubroom and discovers that his fellow first-year, Eru Chitanda, has already become a member. However, despite his obligation being fulfilled, Oreki finds himself entangled by Chitanda's curious and bubbly personality, soon joining the club of his own volition. Hyouka follows the four members of the Classics Club—including Oreki's friends Satoshi Fukube and Mayaka Ibara—as they, driven by Chitanda's insatiable curiosity, solve the trivial yet intriguing mysteries that permeate their daily lives.

For Kanade Amakusa, life as a high schooler should have been normal, and it would have been—if he wasn't living with the most ridiculous curse imaginable. "Absolute Choice," a system forced upon him by a self-proclaimed god, randomly presents a mental selection of actions that he must act out based on his choice. To add to his dilemma, it tends to occur in the most public of places, and his options never seem to deviate from the rude and crude in nature. As a result, the helpless boy stresses through each day, fumbling to repair his already tarnished reputation while desperately praying to avoid the next spontaneous episode of Absolute Choice. To his dismay, the one in charge is always one step ahead of him and proceeds to not-so-subtly "choice" him into the lives of several girls at his school. Just when Kanade's school life can't seem to be doomed any further, a decision that he reluctantly selects on the way home sends a beautiful girl crashing down from the sky, along with the promise of more hysterically hellish choices.

The 1920s was a decade of great change and upheaval, with monstrous demons appearing across America. To combat this menace, the holy organization known as the Order of Magdalene was established. The organization's New York branch is home to the young and reckless Sister Rosette Christopher, as well as her partner Chrno. Tasked with the extermination of demonic threats, the renowned team is excellent at their job, despite causing extensive collateral damage on their missions. However, both Rosette and Chrno are driven by their dark pasts. Through exterminating demons, Rosette hopes to find her lost brother Joshua who was taken by the sinner and demon, Aion, with whom Chrno also shares a bloody history. The two of them must fight off the increasingly dangerous demonic menace and discover its source, while continuing to search for the truth behind Joshua's disappearance.

Daisuke Niwa is a clumsy, block-headed, and wimpy middle school student who has few redeeming qualities. On his 14th birthday, he finally decides to confess his love to his longtime crush Risa Harada, but is rejected. In an unexpected turn of events, however, Daisuke finds himself transforming into Dark Mousy, the infamous phantom thief, whenever his mind is set on Risa. Though Daisuke is unaware of this strange heritage, his mother is certainly not: since before the boy was born, his mother had been planning for him to steal valuable works of art and let the name of the elusive art thief be known. With doubt and confusion constantly clouding his mind, Daisuke finds himself struggling in his relationships with classmates and family. And it is not long before Daisuke realizes that he is not the only one with a fated family legacy—his greatest adversary could be the one classmate he is most unwilling to fight.