From the janitors who replace the toilet paper at Area 51 to the team that gathers intelligence for the Joint Special Operations Command to the most highly trained signals intelligence collectors at the National Security Agency, an enormous amount of taxpayer money is spent trying to keep what these entities do on a daily basis a secret. And for good reason.
But the government often trips over itself to obscure even the basic outlines of secret units, even when in an age of ubiquitous information when it's hard to keep quiet about anything.
About three-quarters percent of the information you'll read below has been compiled from official government sources writing in unclassified papers and on their LinkedIn profiles. The rest comes from my reporting. No real secrets were harmed during the course of this production; I've left out several entities whose very existence is properly (at least to me) classified.
F6 (The Special Collection Service) — In embassies across the globe, National Security Agency analysts work together with CIA teams to intercept signals intelligence (SIGINT) from denied areas — countries the US has to spy on. The folks who work on these teams are part of SCS, a joint CIA-NSA organization. It is not acknowledged by the NSA, although its internal division code, F6, can be found in material released through FOIA requests. If the CIA needs to break into a foreign embassy and bug a room, or set up fancy SIGINT collection equipment in a hotel across from it, its officers will work with SCS members based in the U.S. Embassy.
Ground Applications Program Office — The more anodyne the name is, the more interesting the activities tend to be. GAPO, based at Ft. Belvoir, runs secret technology and procurement programs for Delta Force and for the most highly classified Army intelligence projects. Try to Google it, and you'll come up with next to nothing. But a LinkedIn resume of a former GAPO director says the job is “Responsible for the development, fielding, and sustainment of 190 programs, projects, and equipment evaluations with an annual budget in excess of $500 million, each with its own cost, schedule, and performance standards. Its commander is “[s]elected by senior executives to manage the two top classified programs within the United States Special Operations Command.”
Air Force Flight Test Center, Detachment 3 / 30th Reconnaissance Squadron (Area 51 at Groom Lake / Creech Air Force Base, NV) — Technically, Detachment 3 is based in California. But that's a cover. The men and women of this unit serve as the principle managers of the Groom Lake test site for the U.S. Air Force and the CIA — the dream land known popularly as Area 51. The 30th Reconnaissance Squadron, based at nearby Creech Air Base, tests secret UAV projects at Area 51 and operates many forward deployed hovering sensors, like the RQ-170 drone that crashed in Iran in December.
USAF 1st Helicopter Squadron, Joint Base Andrews, MD — Known by the call-sign “Mussel,” this unit is responsible for carrying out the Air Force's continuity of government mission in the National Capital Region — the evacuation of key civilian government officials. It's very easy to catch a glimpse of one of these UH-1N birds from the Mall in DC. At least two of them are in the air over DC on a near-constant basis.
Unnamed Naval Annex, Potomac River, Washington, D.C. — Its construction in 2003 caused a hubbub in DC: the Navy was building a mysterious and highly classified building smack in the middle of the capital's mall-scape. In order to give their blessing to the the required environmental reviews, members of DC Fine Arts Commission had to be sworn to secrecy about its purpose. A senior U.S official insists that providing the name of the Navy unit that operates the building and linking it to its purpose would constitute a breach of classified information. So all we can say is: it has something to do with highly-secret continuity of government plans in the national capital region.
Special Capabilities Office — When JSOC or the CIA have an acute technology problem, the SCO can help them bypass the regular and time-consuming acquisition process that doesn't keep pace with battlefield requirements. The SCO was set up as a free-floating entity that could find, develop, acquire, research and test – the testing is important, because SCO folks accompany operators onto the battlefield and make sure the stuff works. The SCO is responsible for several formerly classified systems that are now overt, like armed Predator drones and RFID tracking. SCO operates in addition to JSOC's own secret procurement offices (see #4 above), and is considered the “black budget” component of the Rapid Equipping Force, which tries to speed new technology to the entire battlefield. On the Pentagon org chart, the SCO reports to the Deputy Undersecretary of Defense for Advanced Systems and Concepts.
227th SOF (Special Operation Flight) squadron, McGuire AFB, NJ — Members of this unit operate two Foreign Emergency Support Team (FEST) planes that are on stand-by at a moment's notice to deploy U.S civilian intelligence and diplomatic personnel to the scenes of terrorist incidents and world crises.
Army Compartmented Element, Ft. Bragg — Very little is known about ACE, other than its role in providing real-time intelligence to Army special forces. A detachment of ACE, known by the initials BI, is comprised entirely of highly trained female interrogators and intelligence collectors.
486th Flight Test Squadron, Eglin AFB, FL — One of its six squadrons is on stand-by alert for special operations and intelligence missions world-wide; the 427th Special Operations Squadron, based at Pope Air Force Base, has its pilots flying missons for the secret squirrels of JSOC and the CIA.
Mission Support Activity (MSA) — America's unacknowledged 17th intelligence service, it was transferred from the Army to the Joint Special Operations Command in 2003. With an annual budget of around $80 million, MSA gathers intelligence to support the special missions of JSOC's elite units, often operating in areas where the CIA isn't able to tread. MSA has acquired a particular expertise in close-in signals intelligence collection, and they were deployed to Afghanistan in early 2002 under the cover name GRAY FOX. Their cover name, until two three years ago, was INTREPID SPEAR. Within JSOC, they're known simply as “The Activity.” The current code name is classified. By the way: the openly perusable base directory at Ft. Belvoir, VA includes a listing for MSA.