Welcome to the shady world of intelligence work and espionage operations. A world where the enemy is not often clear, and where killing someone doesn't accomplish much except to complicate matters. Where the objective is usually as nebulous as the opponent, and often just part of a larger scheme.
A "special operation" can include assassinations, kidnappings, burglaries, sabotage, smuggling, courier service, full-scale assaults, and bodyguard duty.
The primary feature of "special operations" is secrecy. "Plausible deniability" ceases to be a phrase, moves past being an active term, and becomes a way of life. Evey part of the mission has to be shrouded in secrecy, not just before the mission, but after it, too. In short, a "special operation" means a great deal of trouble just to conceal yourseld and the mission from discovery. And you can't even brag about them, so forget looking to increase your renown among other mercenaries.
Special Operations is a dark twist on the already shady world of Merc: 2000. It includes more information on the organizations that most mercenaries will get to know on a business basis: the CIA, DIA, FBI, KGB, GRU, MI-6, etc. It also includes enhanced combat rules, including rules for nonlethal combat, precision weapons fire, new melee weapons, the effects of antitank weapons on living creatures, and weapon specialization. Of course, Special Operations contains adventures, both for the survivalist world of Twilight: 2000 and the more complex politics of Merc: 2000.