The origins of Special Operations [SO] in Starfleet is shrouded in mystery
that will not become known for decades to come. However, some details have
recently become declassified. During the Cardassian War, the confines of
positional warfare in regards to starbases made normal ship-bourne operations
virtually useless. The first attempts to take Cardassian bases by Starfleet
security teams resulted in very embarrassing and horrendous defeats. The
organization called "Pebble Water", under Defense Operation Plan
[DefOpPlan] 2842, was established to investigate and implement a feasible
special warfare department that could be called on to perform more infantry-based
close-quarters-battle [CQB] and combat intelligence gathering operations.
"Pebble Water" was highly successful, resulting in several critical
victories, although all so classified their details were put into a secret
computer database located on an uninhabited asteroid in the Sol System
that would not reveal its presence for 150 years. At that point it would
send a coded signal to the President of the Federation on a frequency reserved
exclusively by a secret Federation Council order for Black Ops.
After the war, "Pebble Water" atrophied with the demands of peacetime exploration siphoning resources from other military oriented operations. Still some operations were taken during this time, such as the Pegasus project concerning interphase cloaking. It was highly involved in violations of the Treaty of Algeron which was seen by many in Starfleet as a sellout to the Romulans a century back. However, that all changed when the Borg were rediscovered in 2365.
The Prevaricate class starship which had been first experimentally developed during the Cardassian War was thrusted onto the front boiler and made a top priority and all resources that could be siphoned covertly to the project were allocated.
During the Dominion War production was put into full swing. Purposely not put on the publicized front line, the Prevaricates worked far behind Dominion lines and within the Romulan Star Empire gathering much needed intelligence about the increasing unstable neighbor in the Beta Quadrant.
After the end of the Dominion War, the realization by the Federation that Starfleet had become hampered by its venerated exploration emphasis eroded opposition to creating a strictly military defense branch (which critics stated should have been made decades ago since the preamble of the UFP constitution stated "...for the common defense.") After calling the Vespane Conference together, those in SO saw an opportunity for absolution and were some of the heaviest lobbyists for a complete revocation of the Treaty of Algeron. They succeeded.
The immediate benefit was that they no longer worked on an illegal project and were no longer liable for their present crimes. But the Romulans performed even better than SO had hoped. In Article XXI of the Treaty of Vespane, in an act of forgiveness and goodwill, all treaty violations were pardoned and SO was allowed to continue functioning.
The President then set out to organize the new legitimized organization. Now able to be officially called "Special Operations", General Order 3351 established the Department of Starfleet Special Operations to the level of a major divison (equal to Starfleet Exploratory/Colonization, Intelligence, and Military Reserve) that had its Commander-in-Chief Special Operations Command sit on the Joint Chiefs of Staff. General Order 3352 specified that SOC units could be temporarily stationed to Starfleet Exploratory or Starfleet Military Reserve units for situations necessitating the unique skills and resources of special forces where timely communication between branches would be critical to mission success.
General Order 3353 specified the command structure of SOC. Special Operations would be commanded by a four pip admiral, the Commander-in-Chief Special Operations Command [CINCSOC].
Under that would be a three pip position responsible for coordination
and strategy of SO units, Commander-in-Chief Special Operations Command,
Along with that would be another three pip position in charge of coordination of intelligence gathered in the field by SO units and Starfleet Intelligence and the Starfleet Military Reserve Intelligence Office, Commander-in-Chief Special Operations Command, Intelligence [CINCSOC-INTEL].
For recruiting, training, technology, and research, a one pip position would be established, Commander-in-Chief Special Operations Command, Research and (Technological and Personnel) Development [CINCSOC-R&D].
These members form the core of Special Operations Command. They report directly to the Secretary of Defense, although almost all their missions will involve SMR. SMR is nearly always consulted on tactical and strategic options and methods.
There was some initial opposition by some to giving SO such high ranks relative to commanders in adjacent offices that possessed so many more personnel and resources; however, the time-intensive nature of special operations dictated that ranks be assigned in a manner that would confer the best ability to expedite action in the face of intra-organizational opposition to operations that might infringe on missions and resources held by other commanders.
The exact numbers of crews and ships is highly classified. Only five individuals in all the Federation know (the President, the SecDef, CINCSOC, CINCSOC-OPS, and CINCSOC-INTEL). The only known low-classification (classified as "Restricted", "Secret", or "Top Secret") ships known are the USS Shadow Horseman, Apocalypse, Megiddo, and Odysseus. Other ships and crews are classified in compartmentalized codenames and are restricted to extreme high level access (usually fewer than 10 people in the Federation).
All references to the "Prevaricate" class and the "USS Shadow Horseman" are copyrighted David Highlander. They are not public domain and not for use without his express permission and any and all infringements will be prosecuted to the absolute fullest extent of the law.
All references to the "USS Apocalypse" are copyrighted to C. David Sands III. It is not public domain and not for use without his express permission and any and all infringements will be prosecuted to the fullest extent of the law.