Early this month, Vice Adm. Robert Harward—a former commander of the SEALs—the Navy’s elite SOF that recently killed al-Qaeda leader Osma bin Laden—was appointed deputy commander of Central Command, the military region that embraces the Middle East and Central Asia.  Another SEAL commander, Vice Adm. Joseph Kernan, took over the number two spot in Southern Command, which covers Latin America and the Caribbean.

Indeed they do. U.S. Special Operations Command (SOC) admits to having forces in virtually every country in the Middle East, Central Asia, as well as many in Africa, Southeast Asia and Latin America. But true to its penchant for secrecy, SOC is reluctant to disclose every country to which its forces are deployed. “We’re obviously going to have some places where it’s not advantageous for us to list where were at,” Nye told Turse.

SOF forces have almost doubled in the past two decades, from some 37,000 to close to 60,000, and major increases are planned in the future. Their budget has jumped from $2.3 billion to $9.8 billion over the last 10 years

These Special Forces include the Navy’s SEALs, the Marines Special Operations teams, the Army’s Delta Force, the Air Force’s Blue Light and Air Commandos, plus Rangers and Green Berets. There is also the CIA, which runs the clandestine drone war in Pakistan, Yemen and Somalia.

It is increasingly difficult to distinguish civilian from military operatives. Leon Panetta, former director of the CIA, is now Defense Secretary, while Afghanistan commander Gen. David Petraeus—an expert on counterinsurgency and counter terror operations—is taking over the CIA. Both have worked closely with SOF units, particularly Petraeus, who vastly increased the number of “night raids” in Iraq and Afghanistan. The raids are aimed at decapitating insurgent leadership, but have caused widespread outrage in both countries.

The raids are based on intelligence that many times comes from local warlords trying to eliminate their enemies or competition. And, since the raids are carried out under a cloak of secrecy, it is almost impossible to investigate them when things go wrong.

A recent CIA analysis of civilian casualties from the organization’s drone war in Pakistan contends that attacks since May 2010 have killed more than 600 insurgents and not a single civilian. But a report by the Bureau of Investigative Journalism at City University in Londonfound “credible evidence” that at least 45 non-combatants were killed during this period. Pakistani figures are far higher.

Those higher numbers, according to Dennis C. Blair, retired admiral and director of national intelligence from 2009 to 2010, “are widely believed [in Pakistan] and, Blair points out, “our reliance on high-tech strikes that pose no risk to our soldiers is bitterly resented.”

Rather than re-examining the policy of night raids and the use of armed drones, however, those tactics are being expanded to places like Yemen, Somalia, and Libya. The question is, who’s next?

Latin America is one candidate.

A recent WikiLeak release demonstrates that there was close coordination between right wing, separatist groups in eastern Bolivia—where much of that country’s natural gas reserves are located—and the U.S. Embassy. The cables indicate that the U.S. Embassy met with dissident generals, who agreed to stand aside in case of a right-wing coup against the left-leaning government of Evo Morales. The coup was thwarted, but Bolivia expelled American Ambassador Philip Goldberg over U.S. meddling in its domestic politics.

The U.S. has a long and sordid history of supporting Latin American coups—at times engineering them— and many in the region are tense over the recent re-establishment of the U.S. Fourth Fleet. The latter, a Cold War artifact, will patrol 30 countries in the region. Given the Obama administration’s support for the post-2009 coup government in Honduras, its ongoing hostility to the Hugo Chavez in Venezuela, and now the WikiLeak revelations about Bolivia, the idea of appointing a “shadow warrior” the number two leader in South Command is likely to concern governments in the region.

SOFs have become almost a parallel military. In 2002, Special Operations were given the right to create their own task forces, separate from military formations like Central and Southern Command. In 2011 they got the okay to control their budgets, training and equipment, independent of the departments of the Army, Navy, and Air Force. If one reaches for an historical analogy, the Praetorian Guard of Rome’s emperors comes to mind.

There is a cult-like quality about SOFs that the media and Hollywood has done much to nurture: Special Forces are tough, independent, competent and virtually indestructible. The gushy New Yorker magazine story about SEAL Team Six, “Getting Bin Laden,” is a case in point. According to New York Times columnist Maureen Dowd, the story will be made into a movie-for-TV and released just before the 2012 elections.

There is a telling moment in that story that captures the combination of bravado and arrogance that permeates SOF units. An unidentified “senior Defense Department official” told author Nicholas Schmidle that the bin Laden mission was just “one of almost two thousand missions that have been conducted over the last couple of years, night after night.” And then adds that these raids were routine, no big thing, “like mowing the lawn.”

But war is never like “mowing the lawn,” as 38 American and Afghan SOFs found out the night of Aug. 6 when their U.S. CH-47 “Chinook” helicopter flew into a carefully laid ambush just south of the Afghan capital of Kabul.

“It was a trap that was set by a Taliban commander,” a “senior Afghan government official” told Agence France Presse. According to the official, the Taliban commander, Qari Tahir, put out a phony story that a Taliban meeting was taking place. When Army Rangers went in to attack the “meeting,” they found the Taliban dug in and waiting. Within minutes the Rangers were pinned down and forced to send for help.

The Taliban had spent several years practicing for just such an event in the Korengal Valley that borders Pakistan. According to a 2009 Washington Post story—“Taliban Surprising U.S. Forces With Improved Tactics”—the Valley is a training ground to learn how to gauge the response time for U.S. artillery, air strikes and helicopter assaults. “They know exactly how long it takes before…they have to break contact and pull back,” a Pentagon officer told the Post.

“The Taliban knew which route the helicopter would take,” said the Afghan official, because “that is the only route, so they took position on either side of the valley on mountains and as the helicopter approached, they attacked it with rockets.” According to Wired, the insurgents apparently used an “improvised rocket-assisted rocket,” essentially a rocket-propelled grenade with a bigger warhead.

As soon as the chopper was down, the Taliban broke off the attack and vanished. According to the U.S., many of those Taliban were later killed in a bombing raid, but believing what the military says these days about Afghanistan is a profound leap of faith.

SOFs are not invulnerable, nor are they a solution to the dangerous world we live in. And the qualities that make them effective— stealth and secrecy—are in fundamental conflict with a civilian controlled armed forces, one of the cornerstones of our democracy.

As Adm. Eric Olson, former head of Special Operations, recently said at the Aspen Institute’s Security Forum, having Special Forces in 120 countries “depends on our ability to not talk about it,” and what the military most wanted was “to get back into the shadows.”

Which is precisely the problem.