Taken from Okami World Wiki:
Blight arrived in Sei'an shortly after the call of Yami from Kamui and the arrival of Ninetails in Ryoshima. It possessed the Emperor's body, causing him to fall ill and exhibit abnormal behavior. In the meantime, Blight's toxic mist contaminated the entire capital with a deadly disease, causing people to drop dead like fleas. In an effort to keep control of the city, Blight put the Emperor into a coma after having him lock up Kaguya. Blight's reasons for having Kaguya being imprisoned remain a mystery, she was unaware of Blight's existence or any means to harm him.
Blight's microscopic existence was unknown to