You can use the FATE rules to describe Organizations -- the Ninja Clan of the Eye, the Potscrubbers Guild, Joe Patroni's "Family," U.N.C.L.E, whatever. They get Aspects in a standardize structure that lets you see how they interact with each other (or with individuals -- the "High-Tech Minions" Aspect of Hydra might be used in a very broad sense in a contest to see if your spy can infiltrate their headquarters).

This all needs to be further fleshed out here, since I've not actually done this, nor felt the need to (sorry about that), but there's a nice thread by Robert Donoghue on using the same sort of rules for cities and nations that's worth looking at. You could even set up something to let those who hail from a particular country (or organization?) automatically get some Aspects from there.[1]

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Character Rules