This Synopsis was written by me.
For a school project, art student Jin Mikuriya decides to carve a statue out of a piece of wood taken from the sacred tree of Kannagi town. But as he's about to take the statue to school, the goddess of the sacred tree, Nagi, uses the statue as a medium to materialize before him. When Nagi learns that the sacred tree has been cut down and can no longer protect the town from "impurities," she decides to do it herself, employing Jin as her aid since he also has some kind of spiritual power that allows him to destroy impurities.
Because Jin lives alone, with only his fellow classmate and childhood friend Tsugumi looking out for him, he lets Nagi live with him and she eventually starts to attend his school. Since Nagi's powers as a goddess have been weakened, she decides to win over the hearts of the students at school and use their praise to increase her god-like powers. However, her plans become a bit disrupted when her sister Zange, the goddess of another sacred tree, arrives on the scene and also wants to gain the popularity of the people and destroy the "impurities." Jin has his hands full too, trying to keep Nagi's identity as a goddess a secret from his classmates. But as Nagi and Jin get to know each other better, and as Nagi becomes well-liked by the students at school, Jin begins to realize that she has many secrets he doesn't know about. He notices that, from time to time, another personality takes over Nagi, and he is still not clear about what "impurities" are or if Nagi really is the god she claims to be. Although Nagi is adamant about being a god at first, eventually she too begins to question whether she really is a god or not, since her memories before meeting Jin are unclear, and she also does not know who this "other Nagi" that's dwelling inside her is. While they continue to hunt down "impurities" and occasionally have fun with their classmates, Nagi and Jin try to find the answers to the mysteries surrounding Nagi's identity and the origin of "impurities."