The Hidden Village of the Leaf
Please note that this is a VERY loose guide, based entirely on my headcanon for TST, and subject to change whenever other people have other ideas for it. NONE OF THIS IS SET IN STONE. NONE OF IT. It's also all very vague, so you're help is needed! Become a member of the Leaf today!
The Basics
Okay, so technically, in TST, it's not a village, but it is a lot more hidden than it is in canon. In TST, the Leaf, as it's often known, is a fairly secretive organization. Secretive in that, if you don't have the resources or inclination to hire them? You, like as not, do not know about them. While the base is located in one of Ivona's main cities, the organization operates independently of the government of Ivona, accepting contracts from whoever the highest bidder happens to be. Usually, that bidder happens to be Ivonian, but not always.
As for the services you're bidding on? Well, of course, being highly trained professionals, their services vary wild. Everything from escorting the paranoid pawn of the week to offing important officials (though the price for such a thing is probably more than most can afford--the benefit must outweigh their risk, after all), they can do it.
The Agents (aka NINJAS OMG)
TST has ninjas! Yes, they still run on chakra here, and bloodline limits can still come into play, keeping in mind the power restrictions of the setting. Other powers can be gained through SCIENCE, mana crystal abuse, demi-human heritage, or any combination thereof. The one thing everyone who works for the Leaf has in common is that they've chosen to turn those talents towards helping advance the cause of the Leaf (or, at the least, advance the cause of getting their paycheck from the Leaf).
The most important difference from canon is the fact that (since all characters in the RP are one of the ships) the Leaf sends out people a whole lot more frequently, and tends to keep them on longer-term assignments than in canon.
As long as you keep in touch (occasional communication and notice when big shit goes down can probably be hand-waved in as NPC interaction), and don't do anything counter to the Leaf's interests, they fine with whatever you choose to do. Want to go undercover and figure out what Captain Bradley of the Amestris is really up to? Think making trouble (and finding things out) with the crew of the Serenity would be fun? Go for it. Want to train little fledglings the fine art of killing as a weapons master? Jsut don't give away too many secrets.
Of course, not everyone likes secret ninjas: you may find yourself, if your loyalty is to the Leaf, at odds with any of the big governments in TST, including Ivona. Sometimes other people don't take kindly to the notion that anything of interest they do being reported to some shadowy organization. Best not to let that sort find out then, isn't it?
The Leaf also has its renegades, those who have chosen to defect. Actively working against the interests of the Leaf, or seeking the Leaf's dismantling and cessation, well, they don't look too kindly on that sort of thing.
Other Organizations
It's sort of a moot point, since we haven't got anyone from these groups, but some ideas for other groups such as other hidden villages and/or Akatsuki are more than welcome. I personally like the idea of Akatsuki as a terrorist organization looking to bring down all the governments--or perhaps just the Leaf ad other groups like it. Sand, Cloud, Mist, these could all be worked as Leaf-like organizations spread out across Reial.
Let me just reiterate: This is just my rambling head-canon for TST. It is subject to change whenever anyone brings up new and interesting ideas that could work in this setting. None of this is set in stone. Need a reason for a giant demon to be sealed into a kid? We can work it. Ninja dynasties ala the Uchihas or the other bloodlines all fit in here somwhere too. Let's work it out!