Section 31
Secret shadow arm of the Federation government, dedicated to protecting the Federation from inside and outside threats at any cost. Agents of Section 31 either conceal their identities from their families and friends or fake their own deaths to take part in it.
In the 23rd Century, the Section 31 ship Deogen under the command of Agent Talbot went to Ceti Alpha Five in hopes of convincing Khan Noonian Singh to work for them. Instead, it ended up in combat with an Andorian battlecruiser controlled by The Path of Khan and the SS Clydesdale. The ship was destroyed when it crashed into Ceti Alpha Six. Ronnie Harper used her psychic abilities to ensure Section 31 forgot the Deogen existed and never came looking for it. ("The Khan Job" [TOS])
By the 24th Century, Section 31 was using illegal technologies including the phasing cloak, which is installed on all their starships. Section 31 vessels are heavily armed, the more powerful ones even have pulse phasers like those found on the Defiant Class starships. ("Section Thirty-One" [BAN]). The head of Section 31's starfleet had, for some time, been Admiral Jared Newman. After Newman's death, Admiral Raymond Walker was named his successor. ("Dark Horizon", "The Truth Is Out There" [BAN]). Section 31 goes to extreme, although often creative ways to conceal it's existence, usually using the men-in-black fear of being mysteriously 'erased' ("The Truth is Out There" [BAN]). The flagship of the Section 31 starfleet is the USS Banshee. ("Section Thirty-One" [BAN]). Most Section 31 officers are not told of the existence, much less the location of Section 31 headquarters so that any officer who is captured cannot provide such information through a mental probe or similar means. Such was the case with Agent Sloan after he was killed aboard Deep Space Nine. Only the captain of a Section 31 starship knows where headquarters is. ("The Truth is Out There, Part Two" [BAN]).
In the 26th Century, Rosalyn Bain, the wife of Captain Reginald Bain of the USS Anomaly, is a Section 31 agent, a fact that her husband is unaware of. Section 31 tried to recruit her adopted son, Lieutenant Commander Tovar and did recruit her daughter, Audrey Bain.