system
Given the following post, respond as if you're commenting on Reddit:
human
[Star Trek] Does the Federation take part in black ops?
gpt
Short answer; yes.  Longer answer; astonishingly so.  The UFP has elements of Starfleet that work well under the radar for a variety of tactically valid reasons, which is why Starfleet Intelligence exists.  They are what you'd consider most akin to "conventional" intelligence agencies that exist in other power-bases across the quadrant (Romulan Tal'Shiar, Cardassian Obsidian Order, etc).  If you need a 20th century Earth equivalent, SFI is similar to the DIA - the Defense Intelligence Agency - in that it is not a civilian organization, but a military intelligence arm that can operate with a fair amount of independence under the broader umbrella of StarFleet.  They have demonstrated tactical effectiveness on the battlefield and in criminal cases, at one point recruiting Chief Petty Officer Miles Edward O'Brien, then serving as Chief of Operations on the Bajoran owned but Starfleet operated "Deep Space Nine."  He was inserted as a deep cover operative to crack the Orion Syndicate, an exceptionally powerful criminal cadre that operates on the edges of Federation controlled space.  

This, though, is Junior Varsity league.  Lets discuss the big time.  

Section 31.  

While an astoundingly small amount is known about an organization that apparently traces its roots back to the very founding of the Federation, the scope of Section 31 is enormous and the resources are seemingly unlimited.  They were directly responsible for the creation and delivery of a mutagenic bioagent into the population of creatures known as "The Founders," and were so remarkably effective at their duties that The Founders, even with their advanced physiology and technological resources, could not defeat the agent.  During the same time period, there are unusual reports of a "mentally unhinged" StarFleet officer, claiming to be from Section 31, involved in the destabilizing of a senior Romulan Senators career, though he was allegedly summarily executed for his involvement, making the situation hard to decipher.  There are rumors they were involved with the crew of the very first Warp 5 starship (NX-01), specifically with their tactical officer Lt. Malcolm Reed, but very little information can be reliably sourced for their actions.  

The one thing we can reliably state regarding Section 31 is that, as a secret intelligence gathering organization, they have avoided the notice of every other major power in the quadrant and have somehow operated with total impunity for several hundred years without leaving a trace of their operations.  If Section 31 truly exists beyond conspiracy theories and half formed supposition, it represents a covert operations force the likes of which there are no historical parallels for.