The Ainu people of Hokkaido (a completely different ethnicity and language from the Japanse) held out against Japanse rule until 1899. During the Tokugawa period, they where in extensive trade with the Japanese who own the southern portion of the island. I think this is a very realistic possibility for a another faction with it's own culture, traditions, beliefs and military fighting style completely different from the rest of Japan. Being coloured all grey and being named "Ainu rebels" will do them no justice, no justice at all.