Ghostly, primordial beings known as Mushi continue to cause mysterious changes in the lives of humans. The travelling Mushishi, Ginko, persists in trying to set right the strange and unsettling situations he encounters. Time loops, living shadows, and telepathy are among the overt effects of interference from Mushi, but more subtle symptoms that take years to be noticed also rouse Ginko's concern as he passes from village to village. Through circumstance, Ginko has become an arbiter, determining which Mushi are blessings and which are curses. But the lines that he seeks to draw are subjective. Some of his patients would rather exercise their new powers until they are utterly consumed by them; others desperately strive to rid themselves of afflictions which are in fact protecting their lives from devastation. Those who cross paths with Mushi must learn to accept seemingly impossible consequences for their actions, and heal wounds they did not know they had. Otherwise, they risk meeting with fates beyond their comprehension.

Eighteen-year-old Dale Reki is a skilled, kind, and respected traveler, acknowledged as one of the leading adventurers in the city of Kreuz. One day while on the hunt for magical beasts, he comes across a sweet devil girl named Latina. She is alone, dressed in rags, and bears the devils' symbol of a criminal: a broken horn. Concerned for her wellbeing, Dale decides to ensure Latina's safety by bringing her to his home, eventually leading to him adopting her. Latina is sweet, innocent and compassionate, charming Dale beyond his expectations. He begins to enjoy the life of parenthood— experiencing the trials that come with raising a child and coping with the heartache he feels whenever his busy lifestyle as an adventurer parts him from her. Although work and life as a new parent become reassuring constants for Dale, the mysteries surrounding the girl remain. Why was Latina alone in the forest, and why does she harbor the symbol of a criminal? At the same time, Latina also begins to learn about the world and herself as she adjusts to her new life with Dale.

In a world covered by an endless sea of sand, there sails an island known as the Mud Whale. In its interior lies an ancient town, where the majority of its inhabitants are said to be Marked, a double-edged trait that grants them supernatural abilities at the cost of an untimely death. Chakuro is the village archivist; young and curious, he spends his time documenting the discovery of newfound islands. But each one is like the rest—abandoned save for the remnants of those who lived there long ago. For the first time in six months, another island crosses the horizon, so Chakuro and his friends join the scouting group. During the expedition, they find vestiges of an archaic civilization. And inside one of its crumbling remains, Chakuro discovers a girl who will change his destiny and the world inside the Mud Whale as he knows it.

The infamous series of unexplainable murders in Hinamizawa have been solved and the chains of fate have broken due to the efforts of Rika Furude and her friends. Rika believes she has finally obtained the normal and peaceful life she desired with her friends; however, she is proven wrong when the wheels of fate begin turning once again after an unfortunate accident. Rika suddenly finds herself in a perfect world, the constant cycle of brutal killings having never taken place, where all of her friends are content and satisfied. Not wanting to abandon the world that she fought so hard for, she learns she must destroy an essential key to get back. But can Rika abandon the faultless world she is given the chance to live in, after all of her battles have brought her this far?