Nagi was shunned as a child by the people around him because of his telekinetic powers. After he killed his mother by accident and blocked the memory, Nagi was picked up by Brad Crawford of Schwarz. Wanting to learn more about the boy's ESP, Crawford left him under the care of Sister Kaoruko Amamiya, a nun who specialized in treating traumatized children. Ken Hidaka had also stayed at her orphanage for a short time after his own mother's death.
However, the Sister actually was using the children living in the orphanage to commit crimes, controlling them via hypnosis she implanted during their counseling. While Ken was revisting after being reunited with a friend he knew from the orphanage, he met Nagi - and it was during this that Weiss received a mission to target Sister Amamiya. It was Ken who ultimately killed the nun. Nagi witnessed the murder, and as a result of his devastation, he made the church collapse by using his telekinetic powers. From there on he vowed to kill Weiss, and hated Ken in specific.
After the incident, Crawford recovered the boy and sent Nagi to Germany to study at the Rosenkreuz facility for a brief time. Then Nagi started to work with Schwarz to get revenge on the world, for the way everybody treated him when he was a child. He is very solemn and embittered towards life and society.