Machine spirits are born from souls that were particularly machine-like in life. In death, the Atlanteans would bind their souls to etched silicon plates, which formed the basis of their advanced computing technology.
TCU-01 "Nadir" is likely what Nadir will turn into when his fight for his people's liberation finally kills him. Purged of his mortality and pesky emotions, he will likely be even more effective in the eyes of his father.