Takashi Natsume, the timid youkai expert and master of the Book of Friends, continues his journey towards self-understanding and acceptance with the help of friends both new and old. His most important ally is still his gluttonous and sake-loving bodyguard, the arrogant but fiercely protective wolf spirit Madara—or Nyanko-sensei, as Madara is called when in his usual disguise of an unassuming, pudgy cat. Natsume, while briefly separated from Nyanko-sensei, is ambushed and kidnapped by a strange group of masked, monkey-like youkai, who have spirited him away to their forest as they desperately search for the Book of Friends. Realizing that his servant has been taken out from right under his nose, Nyanko-sensei enlists the help of Natsume's youkai friends and mounts a rescue operation. However, the forest of the monkey spirits holds many dangerous enemies, including the Matoba Clan, Natsume's old nemesis. Stretching from the formidable hideout of the Matoba to Natsume's own childhood home, Natsume Yuujinchou Shi is a sweeping but familiar return to a world of danger and friendship, where Natsume will finally confront the demons of his own past.

After seeing enough death and tragedy, the immortal Fushi secludes himself on an island, defending himself from enemy Nokkers. However, instead of attacking Fushi in isolation, Nokkers begin targeting the settlements outside of his reach in hopes of luring him out. Soon, a group known as the Guardians—led by Hisame, the descendant of the deceased warrior Hayase—finds Fushi. Inspired by how Fushi protected Janada Island from the Nokkers years ago, the Guardians have grown a considerable following and are recognized throughout the world. Initially reluctant, Fushi allows the Guardians to accompany him to the site of the Nokkers' recent attack. In their village, Fushi meets a few valuable allies, both new and old. But as the conflict with the Nokkers only leads to more loss, Fushi must find the inner strength to face his inevitable sorrow.

Abandoned by their abusive parents and with only each other to depend on, siblings Utsutsu and Yume Hasegawa find themselves led astray by beautiful red butterflies that have appeared in their world. Unbeknownst to them, these crimson winged heralds trumpet the beginning of a cannibalistic nightmare—a mysterious virus known as Pupa is about to hatch. After succumbing to the full effects of Pupa, Yume undergoes a grotesque metamorphosis into a monstrous creature with an insatiable desire for flesh; Utsutsu, on the other hand, is only partially affected, gaining remarkable regenerative powers instead. Reaffirming the resolve to keep the promise he made to himself years ago, Utsutsu is willing to sacrifice everything in order to always be there for his precious little sister. Pupa tells the story of a loving brother's desperate struggles to save his sister while protecting the world from her uncontrollable hunger.

One day, a man claiming to be a god suddenly hacks a certain school's intercoms, ordering all of its students to team up and prepare to be transported to another world. There, they will be given special skills in the hopes that they become that world's heroes and defeat the Demon King that ravages the land. The initial transfer is a success. However, Seiichi Hiiragi, who suffers from his classmates' constant bullying due to his somewhat undesirable appearance, is left behind as no one is willing to be his teammate. Nevertheless, the self-proclaimed god decides to send Seiichi to the parallel world and lets him join his peers. Unfortunately, this fateful ordeal causes Seiichi to arrive at a location deep in the forest, far not only from his schoolmates but from human civilization as well. Desperately searching for a way to change his predicament, Seiichi's miserable days only seem to continue to worsen. Yet when all hope seems lost, Seiichi discovers a strange fruit known as the Fruit of Evolution—which may be his first step toward a significantly better future.