After foiling a world-threatening plot, Shigeo Mob Kageyama returns to tackle the more exhausting aspects of his mundane life—starting with filling out his school's nerve-racking career form. Meanwhile, he continues to assist his mentor Arataka Reigen and the office's new recruit, Katsuya Serizawa, in solving paranormal cases of their clients. While continuing his duties, Mob also works on gaining more independence in his esper and human lives, as well as trying to integrate better with the people around him. However, new supernatural and ordinary challenges test Mob’s emotional stability and force him to confront the realities around him. As he strives to continue forward on the path to maturity, Mob must resolve his emotional crises and reassess the naivety he has held on for so long.

After surviving a vampire attack, Koyomi Araragi notices that his friend and savior, Tsubasa Hanekawa, has been acting strange. When he happens to cross paths with her on his way to a bookstore and sees she has a bandage on her face, he knows something must definitely be wrong. Araragi wants to help her, but Hanekawa assures him that her wound is just something she received at home and that he should not concern himself with it. But when a white cat with no tail is hit and killed by a car, the pair bury the creature and the real trouble begins. When Araragi later pays a visit to his friend Meme Oshino and recounts the day's events, he is informed what they have buried is actually an apparition, one perfect for Hanekawa in her current state. Tasked with finding his friend to confirm her safety, he discovers that she has attacked her parents, possessed by the Sawari Neko. Now, it is up to Araragi to help Hanekawa as she once helped him.

One fateful day, Yuusuke Urameshi, a 14-year-old delinquent with a dim future, gets a miraculous chance to turn it all around when he throws himself in front of a moving car to save a young boy. His ultimate sacrifice is so out of character that the authorities of the spirit realm are not yet prepared to let him pass on. Koenma, heir to the throne of the spirit realm, offers Yuusuke an opportunity to regain his life through completion of a series of tasks. With the guidance of the death god Botan, he is to thwart evil presences on Earth as a Spirit Detective. To help him on his venture, Yuusuke enlists ex-rival Kazuma Kuwabara, and two demons, Hiei and Kurama, who have criminal pasts. Together, they train and battle against enemies who would threaten humanity's very existence.

Yuuji Kazami is a transfer student who has just been admitted into Mihama Academy. He wants to live an ordinary high school life, but this dream of his may not come true any time soon as Mihama Academy is quite the opposite. Consisting of only the principal and five other students, all of whom are girls, Yuuji becomes acquainted with each of them, discovering more about their personalities as socialization is inevitable. Slowly, he begins to learn about the truth behind the small group of students occupying the academy—they each have their own share of traumatic experiences which are tucked away from the world. Mihama Academy acts as a home for these girls, they are the fruit which fell from their trees and have begun to decay. It is up to Yuuji to become the catalyst to save them from themselves, but how can he save another when he cannot even save himself?