Ninja Notes and Three Rings of Clan Politics
by Marc SaindonShay plays on the fade, slice it like a ninja
Cut like a razor blade so fast
You can't really have "Mystara Japan" without ninjas.
Cinematic ninjas, as I'm not writing a term paper on the historical ones.
In-game, outsiders call them ninjas, while they refer to themselves as Shinobi (male) or Kunoichi (female). Those before Name Levels (9 or 10, depending on which edition you use) are provided with the standard black ninja "pyjamas" (Kuroko outfits) when they go on missions, so that when they are caught they correspond to the expected image outsiders think of when thinking of ninjas. Name-level characters don't have this obligation, so they have a bit of "social stealth" ("this man couldn't be a ninja, he's not in the right costume") to fool authorities or enemies.
As Monks, ninjas are Lawful but certainly do a lot of unlawful stuff with assassination, spying, theft, and sabotage. How does their ethics hold up to this dissonance? By creating a 'us and them' mindset, with those within the Ninja Clan counting as people to be absolutely loyal to, the Ninja Master someone to be absolutely obedient to, and keeping a very strict training schedule they commit to. There is the Outer Ring (non-ninjas, who are fair game) and the Inner Ring (your ninja clan, those who matter), which keeps a Shinobi character from going Chaotic in alignment due to their very Rogue-like activities.
What these Monks fail to grasp is that the leadership also applies this logic on them: the Inner Ring has an Inner Circle of leaders who see lower tier members as unproven, thus expendable. This might create some cracks in the Clan loyalty system, with some Monks eventually ditching their commitment to the Lawful alignment and pursue more Neutral (self-interested) politics instead of the politics they pay lip service to. Some Grand Masters might actually have turned Chaotic, picking up levels as Rogues, and running their Clan as despotic cult leaders who rule on whims and are slowly dropping their facades (other leaders might be accused of this).
When internal politics are too much to handle, rival leaders in the Inner Circle tear the Clan apart, with each side claiming to be the "one true way" and all the others as impostors, trying to rally the loyalty of as much ninjas by playing on their Lawful alignments. This leads cycles of Clans fragmenting into civil war, new Clans emerging, wars of extermination between Clans ("join us or DIE!"), and strange alliances. Assassin's Creed comes to mind for other ideas.
Yasuko would have 3 to 5 active Clans (keep the number odd, to make things a bit of a Mexican standoff in which the action of the PCs are the only thing that will tip the balance) and maybe twice the amount of remnant groups that have survived to a handful ("they have killed our Master, and now as his last students, we must avenge him!"). Yasuko's vast wilderness provides ample room to conceal the various Clan bases.
Myoshima would also have their own Clans (much more than on Yasuko) and the cycle of politics might explain why some Rakastas left Patera to settle on Mystara, or some these Clans could be infiltrators trying to sway Yasukan Rakastas back into the fold of the Myoshiman Empire (meaning that the eventual final ninja showdown with the BBEG could be set on the moon).
Notes:
Ninja
(Image from: https://www.deviantart.com/darkwhite2981/art/Ninja-Girl-001-947084493)