Koyomi Araragi spent his last year of high school helping girls in his town resolve various supernatural afflictions. But now Araragi has departed for university, leaving his friends to fend for themselves against new problems and curses that plague them. Yotsugi Ononoki, once a human corpse and now a living doll, takes residence in Araragi's home, keeping watch over his sister Tsukihi, a girl harboring a mystical secret of her own. As part of her duties, Yotsugi fills Araragi's vacated role as occult expert, assisting others in town with their issues. One of these girls, middle school student Nadeko Sengoku, slowly recovers from her own recent brushes with the paranormal. She avoids returning to school, instead spending time alone in her room and pursuing her dream of becoming a professional manga artist. In order to speed up Nadeko's quest for mastery of her craft, Yotsugi convinces her to create four copies of herself, each representing a distinct aspect of Nadeko's personality. However, the clones refuse to help Nadeko, instead escaping into the town and creating a chaotic mess. Now forced to grapple with her own fractured sense of identity, Nadeko sets out to capture them and resolve her inner conflict.

As a young child, Takashi Natsume believed his ability to see youkai to be nothing but a curse. Now a high school student, Natsume has managed to heal from his old wounds and form unbreakable bonds with humans and youkai alike. Natsume's newfound friendships—including the one with his spirit bodyguard Madara, nicknamed Nyanko-sensei—are often interlaced with his duty to return the names of the spirits written inside the Book of Friends, his late grandmother Reiko's keepsake. While more remarkable youkai reach out to him, Natsume discovers that he still has much to learn about the world that surrounds him.

After an awe-inspiring battle with Ichibei Hyousube—leader of the Soul Society's Royal Guard—the powerful Yhwach moves into the final stage of his master plan. He aims to slay the Soul King, the being whose very existence maintains the status quo of three worlds: Hueco Mundo, the Soul Society, and the realm of humans that Ichigo Kurosaki and his closest friends hail from. Conquering his own bout with the remainder of the Royal Guard, Uryuu Ishida joins Yhwach in his efforts to create a new world in his image. With a flood of resolution and newfound power, Ichigo rushes to stop Yhwach from accomplishing his ultimate goal and save the countless lives within the three existing realms. But Ichigo has a complicated lineage, one that leaves him susceptible to Yhwach's sinister influence. Meanwhile, in a final desperate gambit, Jirou Sakuranosuke Shunsui Kyouraku, the newly promoted head captain of the Soul Society's combat corps, enlists the help of an old enemy whose immense power may turn the tide of battle.

Demonic activity worldwide has significantly increased due to the involvement and corrupt practices of the Illuminati. To combat the unnatural influx of demons, the Vatican Headquarters decides to hold the annual Exorcist Certification Exam early and allow for as many exorcists as possible to take up the mantle. Straight from the Vatican, one of the most powerful exorcists, Lewin Lightning Light, arrives at True Cross Academy to help prepare the students for the exam. The ease and mastery with which Lewin performs exorcisms quickly impresses Ryuuji Bon Suguro, who has lost his ambition to continue his studies, and Lewin surprisingly accepts him as his apprentice. Amid the worsening situation, twin brothers Rin and Yukio Okumura are sent to locate the recently missing exorcist Shura Kirigakure, who seems to be chained to a decades-long contract with a powerful, immortal demon hiding in Aomori Prefecture's dangerous, snowy mountains.