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Commander Watari had such a seemingly sinister-looking appearance- all black dress and a translucent Eye Patch Of Power over a functional eye, despite actually being a friendly, quirky guy. While I'm sure some of it has to do with the kind of public face he wants to present, but more than that, it has to do with RahXephon being an optimistic take-off on Neon Genesis Evangelion. Watari is the Gendo Itkari equivalent particularly given that he is Ayato's father- Ayato's mother is the cold, villainous one of the two, and so his eye patch substitutes for Gendo's creepy shades, but his personality couldn't be more different.