Ichijinsha is collecting the series in tankōbon. The first volume was released on August 9, 2006, and as of June 11, 2012, seven volumes have been released. Each volume comes bundled with a pin-up drawn in a collaboration between Takenashi and other prominent artists. The series was adapted into an anime by A-1 Pictures. Directed by Yutaka Yamamoto, the series ran between October 4 and December 27, 2008.Bandai Entertainment licensed the manga for distribution in North America.
The manga went into hiatus after Eri Takenashi developed a Subarachnoid hemorrhage in early November 2008.Comic Rex's editors's denied the speculation that the fan controversy over Nagi'svirginity caused the hiatus and after undergoing successful surgery, Takenashi noted that she hoped to continue the series after she recovers. The manga resumed with the September 2011 issue of Comic Rex on July 27, 2011, but because of Takenashi's health conditions, three consecutive chapters were released, followed by chapters on an irregular schedule.
Jin Mikuriya, a high school student, builds a small statue out of wood, but before he can bring it to school and turn it in, a girl breaks out of the statue. She introduces herself as the guardian deity of the land. When she discovers that the root of her power, a tree on the land of a Shinto shrine, has been cut down, she panics. However, when Jin is able to remove an impurity from her body, she recruits him to help her purify the land. After searching for more impurities, she is introduced to Jin's childhood friend, Tsugumi Aoba, and to Jin's school. Later, she meets her sister, Zange, and they begin to compete for support.
Zange reveals that she has possessed the body of Hakua Suzushiro and subdues Nagi, promising to defeat her older sister. Jin's timely arrival saves Nagi. While eating breakfast, both Tsugumi and Zange arrive, and the three girls vie for Jin's attention. Jin discovers a fan site and a corresponding fan club devoted to Nagi, and with the support of the students, Nagi becomes a student at Jin's school. Reiri Suzushiro, a teacher at the school, reveals himself as the father of Hakua. Nagi later gets a job to pay for her clothing and amenities, but after being discovered by Jin, she quits.
After being carried home by Daitetsu Hibiki, a member of the Art Club, Nagi yells at Jin when he asks her what happened. When the Art Club and Tsugumi begin to investigate, they accidentally cause a rumor that Daitetsu and Jin are in love to spread. After Tsugumi confessing her mistake to Zange, Zange declares that she will become Jin's girlfriend. Her arrival at Jin's household results in Tsugumi and Jin apologizing to each other for their past mistakes. Later, Jin attempts to dig into Nagi's past, which causes Nagi to fly into a rage and run away when she cannot remember. They make up after Jin finds her and reassures her, and they begin to unearth Nagi's memories together. However, a misunderstanding arises after Jin trips over Nagi and Tsugumi walks in, witnessing the pair in a compromising position.
Jin discovers another side of Nagi: Kannagi. Jin manages to talk to her and Kannagi reveals Nagi's true nature at the expense of Jin's warmth, causing Jin to fall ill. Nagi nurses Jin back to health. Later, the Art Club travels to the beach along with Nagi and Tsugumi, and Zange and Reiri arrive as well. The group is surprised with the arrival of Miyuu, a relative of Art Club vice-president Shino Ōkouchi. When Zange tries to reveal Miyuu as a goddess, she is stripped from her body, causing Hakua to regain control. The gods of the beach area detain Nagi, Jin, Hakua, and Reiri, and try to prove Nagi and Zange's identities as demons. However, Nagi and Jin manage to pass the gods' test, proving their divinity.
The ending of the Beach Arc in which gives more information about who Nagi really is while Hakua's past is shown and how Zange came to possess Hakua's body. Also Akiba wants to draw his own Dojin so the art club helps him out in getting ready to sell it.