It was created nearly at the beginning of the Alliance war.  The Fleet Special Forces are comprised of the SFI (Special Federation Intelligence).  One board every ship should be a representative of this section.  They answer to the captain or the the head of SFI, Commodore Claire Gideon

The ATMOS (Advanced Tactical Marine Operations Squad), a force based on the same principals that on Earth military system had.  Highly trained, tuff, organized force.  They are under the command of Commodore Joseph Blackford when we are, I mean the entire fleet, are in danger.  Each big ships have have a company on board.  The Chief Marine Officer answers to the Captain, and usually are sent first into unknown territory to secure it. 

The third part of the Special Forces are the FIGHTER SQUADRON.   A bit less then a quarter of the fleet is equipped with fighters.  The USS Relentless was one of the first ship to be fitted.  The Fighter squadron, if the fleet is in danger are in the hands of Commodore Joseph Blackford.

Commodore Claire Gideon and Joseph Blackford, are part of the Council of war and/or Federation Council in moments of peace, with Fleet Admiral Aden Iskra and Fleet FO Admiral Robin Wilson.  In the subject of the fleet's goal, all of the parties must be in total agreement in the direction to take.