So, as part of the "second chapter" of the Okami story, after you defeat Orochi, you are helped by the Priestess Rao, who is trying to recover the Fox Rods.
However, after recovering the Dragon Orb, you also find that the Water Dragon swallowed the Fox Rods. This is when you see an apparition of Rao guiding you through a shortcut back to the Imperial Palace, to visit Queen Himiko. Here, you find that Rao has been killed/possessed by the Ninetails.
When is Rao replaced by Ninetails in the storyline?