The "paranormal science" story follows nine idiosyncratic individuals, linked by the "Choujou Kagaku Kirikiri Basara" occult summary blog run by 17-year-old second-year high school student Yuuta Gamon. Little incongruities that occur around these nine eventually lead to a larger, unimaginable event that may alter what is considered common sense in this world.

The publication of a new dictionary titled The Great Passage progresses. Mitsuya Majime, originally from publisher Genbu Shobo's sales department, has been recruited by Kouhei Araki, a veteran editor of the dictionary department who is looking to retire soon. The dictionary department is known internally as the "money-eating insect," but Mitsuya uses his perseverance and attachment to the words in order to become a great editor. Mitsuya, who has poor social skills, finds himself working with another man named Masashi Nishioka, who is able to express himself better.

In the near future, most of mankind now lives in a handful of city states. There, for the privileged elite, life should be perfect. But for young Sion, life has become a nightmare since letting a strange boy spend the night in his apartment. Banished to the outskirts of the city, Sion now finds himself in worse danger as his inquiry into a new series of mysterious deaths results in his being arrested on suspicion of murder! Now, on the run, the two young men have only one chance at survival.

First-year high schooler Midori Asakusa loves anime so much, she insists that "concept is everything" in animation. While she spends her time doodling endless ideas and settings in her sketchbook, she hasn't taken the first step to creating anime, insisting that she can't do it alone. After Asakusa's money-loving best friend Sayaka Kanamori notices her genius and drive – and when it becomes clear that their classmate and charismatic fashion model Tsubame Mizusaki wants to be an animator – the energetic trio start an animation club. Together, the three aim to realize the "ultimate world" that exists in their minds, as they come to see the power that fiction and imagination have on their lives and the world around them.

Born into a world 1000 years in our future, Saki and her friends live in utopia. Not only is their idyllic community overflowing with resources, but technology is obsolete, thanks to a magical power that grants the ability to materialize anything. However, when Saki discovers a lost artifact, the facade is shattered! Faced with a startling truth about their town, Saki and her companions face dangers they never knew existed, and their choices may change the fate of everyone.

In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations. Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Can Phos's seemingly mundane assignment lead both Phos and Cinnabar to the fulfillment they desire?

Nadeshiko, a high school student who had moved from Shizuoka to Yamanashi, decides to see the famous, 1000 yen-bill-featured Mount Fuji. Even though she manages to bike all the way to Motosu, she's forced to turn back because of worsening weather. Unable to set her eyes on her goal, she faints partway to her destination. When she wakes up, it's night, in a place she's never been before, with no way of knowing how to get home. Nadeshiko is saved when she encounters Rin, a girl who is out camping by herself. This outdoorsy girls story begins with this first encounter between Nadeshiko and Rin.

One day, Naho Takamiya receives a letter written to herself from ten years in the future. As Naho reads on, the letter recites the exact events of the day, including the transfer of a new student into her class named Kakeru Naruse. The Naho from ten years later repeatedly states that she has many regrets, and she wants to fix these by making sure the Naho from the past can make the right decisions—especially regarding Kakeru. What's more shocking is that she discovers that ten years later, Kakeru will no longer be with them. Future Naho asks her to watch over him closely.

Ginko, a Mushi master, travels from place to place researching the Mushi and helping people who are suffering because of it.

When Yadomi Jinta was a child, he was a central piece in a group of close friends. In time, however, these childhood friends drifted apart, and when they became high school students, they had long ceased to think of each other as friends. One of the friends from that group, Honma Meiko, now has a wish she asks Jinta to fulfil. The problem is, she can't remember what her wish is anymore.

Oreki Houtarou is a minimalistic high school boy. One day, he joins the Classic Literature Club at his elder sister's request. There he meets Chitanda Eru, Fukube Satoshi, and Ibara Mayaka. Chitanda is a calm beautiful girl but she turns into an embodiment of curiosity once she says, "I'm curious." Fukube is a smiling boy with a fantastic memory who calls himself a database. Ibara is a short girl and is strict with others and herself. They begin to investigate a case that occurred 45 years ago. Hints of the mystery are buried in an old collection of works of the former members of Classics Club. The collection is titled "Hyouka."

In an alternate version of the present, Tokyo has been decimated by a shocking terrorist attack, and the only hint to the identity of the culprit is a bizarre video uploaded to the internet. The police, baffled by this cryptic clue, are powerless to stop the paranoia spreading across the population. While the world searches for a criminal mastermind to blame for this tragedy, two mysterious children - children who shouldn't even exist - masterfully carry out their heinous plan. Cursed to walk through this world with the names Nine and Twelve, the two combine to form "Sphinx," a clandestine entity determine to wake the people from their slumber - and pull the trigger on this world.