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In the sometimes morally questionable world of Starfleet Intelligence, the term Black Op is used to describe any operation that cannot, for whatever reason, be known to have either existed or be traced back to the Federation. Types of Black Ops can range from clandestine reconnaissance to Wet Work. Sometime prior to 2370, Starfleet Intelligence devoted an entire section to planning and carrying out these types of operations. The officer in charge of these operations was Rear Admiral Willy Hoyt. (Star Trek: The Nomad Frontier)
Since Section 31 is an independent organization that does not report to Starfleet Command or the Federation Council, their activities would not fall under this category, even though their activities may have a similar interest or goal.