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High school student Jin had seen the kami of the sacred Nagi tree of the local shrine when he was playing nearby as a child. Years later when it was cut down after the shrine was closed, he carved a part of the sacred tree's trunk into a life-sized statue of the goddess, enabling her to enter into it and take physical form, using it as her vessel. Calling herself Nagi after the tree, she tells Jin that the tree had protected the area and that calamaties would ensue unless she could exorcise the impurities (ã‚±ã‚¬ãƒ¬, kegare) that were arising. In a device reminiscent of Mushishi, these impurities take the form of shadowy insects and creepy crawlies. Nagi moves in with the teenage Jin and comedy ensues, especially when his childhood friend Tsugumi (who is supposed to be keeping an eye on him for his father), finds the pretty and apparently teenaged girl living there.
Things get more complex when Nagi takes an interest in attending Jin's school and goes on to discover she is not the only kami to have adopted human form and have the idea of becoming an idol: an offshoot of her god-form that she refers to as her younger sister has also taken human form and become a popular local cosplay idol called Zange-chan. Rivalry between them develops, and students at Jin's school start a fanclub for Nagi, complete with a website (which actually exists: www.nagisama-fc.com).
The series is to a large degree episodic and character driven, living up to the "Crazy Shrine Maidens" moniker more than its Shinto premise. As such it falls into the "goddess (or alien with godlike powers) moves in with teenage boy" genre of anime sitcom, other examples being Oh! My Goddess and Urusei Yatsura.