Skull was almost killed when the 00 cyborgs entered Black Ghost's Base (what they thought was Black Ghost HQ until later in the manga and anime) and set explosives leaving 009 and Black Ghost to fight one-on-one. It is revealed that Black Ghost is not only a cyborg, but a highly advanced cyborg, soundly defeating 009 using his superior acceleration mode. Only a last ditch effort managed to save the nine cyborgs (009 held on to Black Ghost whilst plummeting into what looked like a vat of liquid nitrate and then 001 teleported 009 to safety).
It is not known how Black Ghost survived the explosion. In addition to Black Ghost apparently being a cyborg himself, the true leaders of the Black Ghost Organization turn out to be three brains. Although the 3 brains were destroyed in the end, they claim to be only a part of the entire Black Ghost organization and that the Black Ghost organization were universal and they were just the leaders of the Earth branch of Black Ghost.