A teenage boy, Takashi Natsume has had the ability to see spirits, but he hasn't known the way of dealing with them. One day, he is chased by a spirit, and run into a shrine. Then he encounters another spirit in Chinese-lucky-cat shape.
Natsume inherited "The Book of Friends" from Reiko, his grandmother, and decides to return the name to the spirits. A spirit Tsuyugami come to see him soon, to return his name. But the page with his name had stuck to the next page.
Natsume participates "trial of courage" in the class at the abandoned school building where a spirit has appeared. The class president Sasada is vaguely aware of Natsume's secret.
Natsume finds a train ticket from Reiko's belongings. When he arrives at the station written on the ticket, there is a furry spirit named Santo waiting for Reiko.
Natsume finds a town that had been submerged in water; Natsume gets possessed by a yokai and falls unconscious. Tarusaru informs Natsume about a festival and a Yukata that can turn a spirit into a human for a day.
Natsume who went to study training camp rescues little fox spirit from bullying spirits. The little fox spirit knows that Natsume has "The Book of Friends", he wants to be a follower of Natsume.
Natsume and Nyanko-sensei came seeing fireflies at a certain swamp. They find a strange couple, a man who looks at the swamp and a female spirit who is close to him.
Natsume have been cursed because he saw an evil spirit who was eating spirits. He decides to break the curse without involving his precious people and spirits.
