The Special Forces was created in an attempt by the U.S. government to destroy the Black Dragon organization. It was lead by Sonya Blade and Jax. It was extremely successful in capturing Black Dragon operatives, however, it's leader, Kano, proved to be extremely elusive.
After Shao Kahn failed to take over Earthrealm after the events of Mortal Kombat 3, Sonya and Jax were given permission to form the Outerworld Investigation Agency, a subsidiary of the Special Forces. It's job was to locate portal between Earth and other realms and prevent any future threats.