Painted in red, the word VON is all that is left behind after a terrorist attack on a nuclear facility in Japan. The government is shattered by their inability to act, and the police are left frantically searching for ways to crack down the perpetrators. The public are clueless—until, six months later, a strange video makes its way onto the internet. In it, two teenage boys who identify themselves only as Sphinx directly challenge the police, threatening to cause destruction and mayhem across Tokyo. Unable to stop the mass panic quickly spreading through the city and desperate for any leads in their investigation, the police struggle to act effectively against these terrorists, with Detective Kenjirou Shibazaki caught in the middle of it all. Zankyou no Terror tells the story of Nine and Twelve, the two boys behind the masked figures of Sphinx. They should not exist, yet they stand strong in a world of deception and secrets while they make the city fall around them, all in the hopes of burying their own tragic truth.

At only 12 years old, Takumi Harada is already hailed as a prodigious baseball pitcher. But when his family moves to the backwater town of Nitta, Takumi has no choice but to join his new school's unskilled baseball team. This development has little effect on the boy, as he believes it is more interesting if this no-name club becomes a powerhouse due to his presence. However, due to his overwhelming talent, Takumi is in need of a catcher able to keep up with his pitches. His worries are soon put to rest after meeting Gou Nagakura. As his fan and fellow student, Gou is eager to prove that he is not a simple braggart, but rather a player skillful enough to catch Takumi's pitches. Amid struggling to form a battery with Gou, Takumi comes into conflict with his new teammates due to his irreverent personality but grapples to find the true joy of the sport under his grandfather's guidance.

When tragedy is about to strike, Satoru Fujinuma finds himself sent back several minutes before the accident occurs. The detached, 29-year-old manga artist has taken advantage of this powerful yet mysterious phenomenon, which he calls Revival, to save many lives. However, when he is wrongfully accused of murdering someone close to him, Satoru is sent back to the past once again, but this time to 1988, 18 years in the past. Soon, he realizes that the murder may be connected to the abduction and killing of one of his classmates, the solitary and mysterious Kayo Hinazuki, that took place when he was a child. This is his chance to make things right. Boku dake ga Inai Machi follows Satoru in his mission to uncover what truly transpired 18 years ago and prevent the death of his classmate while protecting those he cares about in the present.

Kouhei Araki, a veteran editor of the dictionary editorial division at Genbu Publishing, plans to retire in order to better care for his ailing wife. However, before retiring, he must find a replacement to complete his latest project: a new dictionary called The Great Passage. But no matter where he looks, he cannot find anyone suitable, as making a dictionary requires a wealth of patience, time, and dedication. Mitsuya Majime works in Genbu Publishing's sales division, yet he has poor social skills and an inability to read the mood in most situations. In spite of this, he excels at having an enthusiasm for words thanks to his love of reading and careful personality. It is these skills that draw Araki to him and prompt him to offer Majime a position in the dictionary editorial department. As Majime accepts his new position, he finds himself unsure of his abilities and questioning whether he will fit in with his new co-workers. Yet amid the vast sea of words, The Great Passage will bring them together.