Colonel Kunugi is the Commander of TERRA. He is a man haunted by his past; during the First Mu War he was directly responsible for his daughter's death. His wife divorced him.

Kunugi is uncommonly friendly to his subordinates, and tolerant of Ayato; he is friends with many influential people in the RahXephon project, including the Professor. He also sees Quon as something of a daughter-substitute. Still, his past actions goad him to seek redemption and he does not want to repeat his mistakes.