As with its prequel, Zoku Natsume Yuujinchou is about Takashi Natsume, a boy who has had the ability to see youkai since he was young, and his bodyguard youkai Madara, nicknamed Nyanko-sensei. Natsume attempts to return names written in his "Book of Friends" (which he inherited from his grandmother Reiko) to youkai in his village. Throughout these adventures, he meets some youkai that are friendly, some that want to steal the Book, and some that want to kill him, as Natsume learns about himself and his relationship with these mysterious beings along the way.

As a lionhearted boy who can’t wield magic strives for the title of Wizard King, four banished Wizard Kings of yore return to crush the Clover Kingdom.

Yuuki Oojima is a member of his high school's Food Research Club, whose main activity is eating snacks bought with funds allocated to them by the school. However, this peaceful and wasteful lifestyle is under threat as the upcoming student election draws near. Satsuki Shinonome, a major candidate and the head of the department of financial affairs, campaigns on a platform that includes disbanding meritless clubs such as the Food Research Club and redirecting their budgets to proper ones. Understandably, the Food Research Club is in an uproar over this development, with president Chisato Sumiyoshi vowing to preserve it. But what can they even do to stop the highly competent and popular Satsuki from getting elected? [Written by MAL Rewrite]

The world as we know it is actually just half the story, as Takeshi Nanase finds out abruptly one summer morning. On his way to kendo practice, Takeshi comes across an unconscious girl in a uniform he doesn't recognize. Takeshi does the decent thing and saves her, and in return the girl wakes up and accidentally turns him into a magic-user. As Takeshi finds out, there is the world he lives in and the world of magic users. Most magic users just want to peacefully coexist with non-magicians, but there are some with bigger ambitions. Mui Aiba is a magician enrolled in the Subaru Magic Academy, where magic users can learn to control and channel their powers and how to live in peace with regular humans. After his fateful encounter with Mui, Takeshi and his newly magician friends Kurumi Isoshima and Kazumi Ida decide to enroll in the Magic Academy as well. All three friends have different reasons for fighting on, whether they're fighting to escape the past or catch up to the future. They wield different kinds of powers, which they must learn to harness in order to fight off the Ghost Trailers, a group of magicians who are willing to use violence to assert their superiority over humans. Pursued by the Ghost Trailers, Takeshi and his friends must train to become stronger, face the leader of the Trailers, and prevent the beginning of the Second Great Magic War.