The Beginning
We learn of Nakago's past in the final episode of Fushigi Yuugi. At the moment of his death his memories are viewed by Tamahome. Nakago belonged to the Hin tribe, which had come from the west and had the physical characteristics of blue eyes and blond hair. They were hated by Kutou's native inhabitants and face prejudice daily. When Nakago was a young boy a campaign was carried out to completely destroy the Hin race. He witnessed his friends dying in front of him as the Kutou soldiers attacked. Nakago's own mother was captured and raped by a group of men. As he was held and made to watch this the power of Seiryuu awakened inside the boy. Without knowing what he did he unleashed a blast of power which killed his mother and the soldiers.
Nakago was brought to the Kutou palace. Since he was a Seiryuu seishi he could not be killed, but the Emperor took a liking to the pretty young boy. For years the Emperor sexually abused Nakago. In time Nakago joined the army and eventually rose to the rank of Shogun, vowing to use his powers to destroy Kutou and have his revenge.
Nakago's goal is become a god through one of Yui's wishes from Seiryuu. He hopes to build a better world to live in and to avenge his people.