Despite the recent Akuma attack, the members of the Black Order are in high spirits as they set about moving to a new base. Immediately upon his arrival, however, Allen Walker is suddenly called by the Central Agency and has his arm forcefully sealed by the Order. He is then led to a surprising meeting with his master, General Cross Marian, who reveals staggering secrets surrounding the enigmatic 14th Noah. A phantom thief incident, the arrival of a mysterious group of Exorcists, the death of an important comrade, and an all-out battle against the Noah Family—just what does this mean for Allen, Yuu Kanda, and the rest of the Order? This is but the beginning of a series of strange, seemingly unconnected events that lead to something far greater.

Blessed with eyes that are able to perceive the otherwise invisible youkai, Takashi Natsume hides his ability from his newfound family and friends to protect everyone's peaceful daily life. Nonetheless, Natsume never fails to show the same kindness to the benevolent youkai and happily returns their names by using the infamous Book of Friends he inherited from his late grandmother, Reiko. Meanwhile, the exorcist clan Matoba still wishes for Natsume to join their ranks due to his overwhelming gift. However, Natsume firmly rejects the clan's invitation since not all exorcists are as reasonable as his friend Shuuichi Natori, and many improperly and indiscriminately seal away every youkai in their way. Unsatisfied with Natsume's answer, Seiji Matoba blackmails Natsume into attending a grand gathering of powerful exorcist families. Natsume soon finds himself in the company of dangerous people and youkai alike. But even then, he continues to defy the exorcists' hard-handed methods and believes that peace between both worlds is possible.

Takashi Natsume has grown accustomed to his encounters with youkai through the Book of Friends, which contains the names of youkai whom his grandmother, Reiko Natsume, has sealed in contracts. These encounters allow Natsume to better understand the youkai, Reiko, and himself. The Book of Friends is a powerful tool that can be used to control youkai; it is sought after by both youkai and exorcists alike. Natsume just wants to live out his daily life in peace but is constantly disrupted by these experiences. If he is to end this torment, Natsume must explore more about the book and the world of exorcism, as well as begin to open his heart to those who can help him.

The entire countryside comes to a halt midday to witness a rare solar eclipse that is rumored to allow the average person to see Mushi. Unable to avert their gaze, the air is full of awe and wonder—but those who know the Mushi are preparing for the eclipse's aftermath. Based on a prediction from Tanyuu Karibusa, the cursed recorder, Mushishi Ginko finds himself in a very unlucky farming village. Immediately following the solar eclipse, a strange black cloud begins to gather in the sky and blocks the sun once more. Suspecting it to be the work of a Mushi known as Hihami, Ginko seeks to liberate the village from perpetual darkness. However, it seems that not all of the villagers are eager to return to the light.