Head: Star Wars Lumiya
Rest: 25th Comic Pack Snake Eyes

As most Joe fans are aware, the Black Dragon Ninja clan were brainwashed by Dr. Mindbender to serve Cobra in case the Arashikage clan ninjas ever revolt. Storm Shadow discovered this, and used his own mind control technique to overwrite the brainwashing of the Black Dragon Leaders. Currently, the Black Dragon Ninja clan act as if their allegiance is to Cobra, but in reality, they are loyal only to Storm Shadow.
(Adapted from the GI Joe wiki)

A Grey Ninja is nothing more than an apprentice in the Black Dragon Clan. They serve the Black Masters, currently under the control of Storm Shadow, but believing they are actually serving Cobra's needs. Should anything happen to Storm Shadow, there would most likely be a breakdown within the Black Dragon Clan, as the masters would become Ronin.