Section 31 is the Federation's top intelligence unit.
They are so secret, that officially, they don't even exist!
Because of this, they do not have any buildings that they operate from, (Like Starfleet Headquarters etc.) there are no official documents that mention them (Other than the Federation charter, and even then you have to know precisely where to look) and there are very few people that even know of their existance.
Section 31 operate as both internal and external affairs. They are charged with protecting the Federation's interests - at ANY cost. They answer to NO ONE, so they are even able to break any Federation rule, law, or civil rights, if it means the survival of the Federation.
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As far as I know, the first time Section 31 was ever mentioned, was in the DS9 episode 'Inquisition', which aired in 1998. Since Men in Black was out in 1997...well, you decide who copied who.
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Scatter has included section 31 in his Star Trek fanfic, Illustrious. They're a good read, and whilst obviously not canon, they might explain things a bit for you - and show just what lengths they will go to, to ensure the safety of the Federation.
