As Kutō's highest ranking general, Nakago commands two thirds of Kutō's army. The last of the Hin Tribe—a people destroyed at the orders of the Emperor of Kutō—Nakago was captured after seeing his mother being raped by Kutō soldiers; the trauma of seeing this triggered his powers and killed the soldiers and his own mother. With the surviving soldiers recognizing him as a Celestial Warrior, Nakago was brought to the Emperor where his natural beauty resulted in his being sexually abused by the Emperor. As he mastered complete control over his abilities, he eventually became a seemingly loyal soldier of Kutō, with the Emperor unaware that Nakago has been planning to betray him all his life.
Once he finds Yui, Nakago manipulates her by letting her believe she was raped so that he can become the person she depends on. He uses her to gain the power of Seiryū, originally intending to take over the world. After learning about the real world that Yui and Miaka come from, he changes his goals to take over it, desiring above all to be a God who controls everything. He uses his powers to go to the real world, where he tries to take over the world. Realizing her mistake, Yui frees Suzaku and Miaka uses her wishes to seal Seiryū, returning Nakago to normal. Surrendering to defeat, he is killed by Tamahome.
Yu Watase notes on several occasions in the chapter notes, as well in the second installment of the omake "The Tale of the Forbidden Women's Hot Spring" from the series 1 OVA (as stated by Nakago himself), that Nakago is her favourite character.