An art student named Jin Mikuriya carves a statue from the wood of the Kannagi tree only to have the statue come to life in the form of a goddess, who has now taken over the statue. He and "Nagi" work together to destroy the impurities that are gathering in the town.
Yuichi Aizawa returns to this city after seven years. In his childhood, he often visited it, but something happend in the past which caused him to block out his memories of the events of seven years ago. On the day after he gets settled in, he meets a girl carrying a backpack with wings on it. Her name is Tsukimiya Ayu and he begins to recall the memories he had lost.