Dr. Ayanokoji admires his creation - An Angel Heart Prototype Code Mark II named Kurumi. This experiment of his is the result of his efforts to save the world. Meanwhile, Nakahito is coerced into entering a mad doctor's mansion that supposedly has the detached living head of a dissected woman in the basement. The eleven-year-old Nakahito is drafted by his peers because he comes from a family of mystics, those who practice the Onmyou way. Dr. Ayanokoji, Kurumi and Nakahito are about to cross paths for the first time in a dramatic way.

Dr. Amagi attempts to coerce Dr. Ayanokoji into working with the Japanese military. When Amagi mistakenly grabs Nakahito, Kurumi rescues him. Nakahito and Dr. Ayanokoji discover they have another mutual associate. Kurumi displays jealousy when Nakahito hugs Kamahito. Dr. Ayanokoji and Kamahito misunderstand Nakahito’s explanation of Kurumi’s activation. Kurumi continues to question why she should proffer any significance to Dr. Ayanokoji. Dr. Amagi discovers another secret within the mansion.

The Imperial Army's preparation for the second Steel Angel's completion draws closer, during which Nakahito finds himself haunted by the words of Dr.Ayanakoji stating that only Nakahito has control over Kurumi. To make matters worse Nakahito is visited by some familiar characters,the end result leaving Nakahito even more confused and Kurumi afraid that her beloved master hates her. As though we thought things could not get much worse it seems the newly activated Saki is well on her way to causing trouble for Kurumi.