The Tokugawa Shogunate
Pro-government Tokugawa forces. Everyone roleplay character is part of the Tokugawa faction since you all attend a school controlled by the government. The Tokugawa are the current shogunate of Japan and rule most of the nation through alliances, marriages, and superior military strength. A 400 year old dynasty that at times has gone from extremely corrupt to absolutely caring for it's people based on who the current shogun was.
A term generic term used to cover monk/peasant rebellions. Warrior monks and priests are fierce fighters. It is a rising movement among the people to completely do away with the lord system. They are an underground rebel movement that has spread all through out Japan. You can not play as an Ikko but your character can sympathize with them.
Long time rivals of the Hattori clan that serve the Tokugawa. When the Tokugawa gained power the Hattori used their place in the new government to slaughter their long time rivals, the Koga. Now rumors and whispers exist of the Koga ninja beginning to gather rebuild. No one knows if these rumors are true or not. You can not play a Koga Ninja.
The head priestess of the shrine at Ise serves the royal family, not warring samurai clans or factions. Ise is a safe place for rest, medicine, and possibly magical instruction.
Wokou Pirates While supposedly hired by Choshu the wokou are famous Asian pirates that will freely raid ships and coastal areas. They are said to have bases in Southern China and the Philippines. Unplayable.
Lesser Ninja Clans
Fuma, Iga, Koga, these are the major ninja clans of Japan. Multiple smaller clans exist however and can be asked for assistance or to attack another person. Be warned though, all ninjas come with a price.