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.

Having spent time at a juvenile corrections facility, teenage delinquent Saki Asamiya is given a chance to redeem herself and delay her mother's possible death sentence by working as an undercover cop. Armed with nothing but a special yo-yo, Saki's assignment is to return to her high school and investigate on the corruption and mysterious deaths among the students. But in order to find the answers to the condition of her school, she must confront the wealthy and powerful Mizuchi sisters, who moved in and have taken control after her previous expulsion.

Unidentified creatures "Archon" suddenly appear and bring the human beings to a crisis of extinction. A special corps "Goulart Knights" is formed to counter attack Archon. The knights have supernatural power to generate "Holy Grail" from their spirits and battle against Archon.

St. President school is one of the most wealthy schools around. Everybody in that school respects the Yukan club, the most popular and richest group in the school. This includes Shouchikubai Miroku, Kenbishi Yuuri, Kikumasamune Seishirou, Hakushika Noriko and Kizakura Karen. They go through dangerous adventures to save their school, and of course, just to kill their spare time.