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.

The lives of high school freshmen Haruki Mishima and Towa Honda revolve around studying, clubs, and girls. Amid their hectic routines, romance is certainly budding for the two best friends. Since childhood, Haruki has been pining over Miharu Mashiki, and a chance encounter at the convenience store reignites his feelings. As for Towa, the class representative Mami Mihashi has caught his eye; but unfortunately for him, his affections are not reciprocated. While Haruki's more reserved approach to pursuing Miharu contrasts Towa's persistence with Mami, love seems to be elusive for both. As the months fly by, only time will tell if romance is in the cards for the duo.

Hotaru Tachibana has a strong sense of justice and just cannot help confronting those who choose to perform malicious acts. Furthermore, Hotaru is actually a girl who likes to disguise herself as a boy. After hearing rumors that her best friend was tricked by the popular host of a local club, Hotaru seeks to punish the evildoer. Upon arriving at the club, however, she is challenged to a so-called "survival game" by the host Masamune Matsuoka, where the first person hit by the bullet of a toy gun will lose. After a destructive fight which results in Hotaru's loss, Masamune forces the young "boy" to join his survival game team named Toy Gun Gun, in order to repay the cost of the damages that "he" has caused inside the club. Although she is initially unhappy with this turn of events, Hotaru quickly begins to enjoy what survival games have to offer and is determined to pay off her debt, much to the dismay of Tooru Yukimura, the other member of Toy Gun Gun. As time goes on, Hotaru begins to develop a close friendship with the rest of the team and hopes to take part in realizing their dream of winning the Top Combat Game (TCG), a tournament to decide the best survival game team in Japan. Although Hotaru tries her best, there are just two little problems: she is absolutely terrible at the game, and Toy Gun Gun doesn't allow female members on their team!

Kino, a 15-year-old traveler, forms a bond with Hermes, a talking motorcycle. Together, they wander the lands and venture through various countries and places, despite having no clear idea of what to expect. After all, life is a journey filled with the unknown. Throughout their journeys, they encounter different kinds of customs, from the morally gray to tragic and fascinating. They also meet many people: some who live to work, some who live to make others happy, and some who live to chase their dreams. Thus, in every country they visit, there is always something to learn from the way people carry out their lives. It is not up to Kino or Hermes to decide whether these asserted values are wrong or right, as they merely assume the roles of observers within this small world. They do not attempt to change or influence the places they visit, despite how absurd these values would appear. That's because in one way or another, they believe things are fine as they are, and that "the world is not beautiful; therefore, it is."