Federation Secret Service
The Federation Secret Service, or F.S.S. in short, was founded in the year the United Federation of Planets was born, in 2161, with as main purpose: to identify and neutralize internal and external threats.
The first Commanding Officer of the F.S.S. was John Mole. He remained C.O. of the F.S.S. until Zack Mannion discovered that he was leaking information to the Klingons. This is NOT publicly known and is forever classified. The only one able to lift that classification is the President of the Federation himself, and he has no intentions to do so, ever.
The F.S.S. is also the largest intelligence organisation in the Federation to this day. Yet, it has kept its secrecy pretty well, even if it is not an organisation that is classified, as is the case with Section 31. The main difference between Section 31, and the F.S.S., is that Section 31 operates within the Starfleet organ, while the F.S.S. directly and ONLY responds to the President. One is allowed to know about its existence, but there it ends. All other information about the F.S.S., its activities, missions, ships, number of employees, and where their activities are located, is strictly confidential. Not even the highest admirals know the exact number of crew and ships.
The F.S.S. has a large number of ships that are heavily armed and shielded. They also have good impulse drives, and even a TransWarp generator is standard for all ships. The F.S.S. has not used warp drive since the beginning of 2300. The crew of their ships and stations are also highly motivated, although not fanatical, as the rumours say about Section 31. The F.S.S. stations have no real design, they are usually built inside asteroids and other big rocks in space. This way, it is actually not possible to know if there is a F.S.S. station in the area or not, especially when there are many asteroids in that region.