The full scale of the shadow war is just coming out now, as detailed in "Dirty Wars: The World Is A Battlefield" by investigative journalist and New York Times bestselling author Jeremy Scahill.

Directed by Vice President Dick Cheney and Defense Secretary Donald Rumsfeld, the White House expanded the Joint Special Operations Command (JSOC) into a global capturing and killing machine.

JSOC, which includes troops from a variety of America's best units, grew from fewer than 2,000 troops before 9/11 to as many as 25,000 today.

While most of their missions remain classified, JSOC operators have been used far more aggressively in the past decade than ever before.

"Their real days of glory ... really only started after 9/11," Colonel Walter Patrick Lang, who spent much of his career in covert operations, told Scahill. "They didn't do a lot of fighting before that."
Known within the covert ops community as ninjas or "snake eaters," JSOC operators train to track a target, fix his position, and then finish him off without being detected.

"They're the ace in the hole," General Hugh Shelton, chairman of the Joint Chiefs of Staff under President Clinton, told Scahill. "If you need someone that can sky dive from thirty miles away, go down the chimney of a castle, and blow it up from the inside — those are the guys you want to call on."

The command was "created in secrecy to perform operations that were kept hidden to virtually all other entities of military and governments," Scahill writes, and the White House took full advantage of that.

From "Dirty Wars":
It was the beginning of what would be a multiyear project by Rumsfeld and Cheney to separate this small, elite, surgical unit from the broader chain of command and transform it into a global killing machine.
What they developed looked like a paramilitary CIA, according to Scahill's reporting.
 By late 2002 JSOC operators were discreetly based in Qatar and Kenya for potential missions in Yemen and Somalia. It developed an in-house signals intelligence unit, known as the Activity, and Rumsfeld created a JSOC human intelligence collection operation, called the Strategic Support Branch, that mirrored the capabilities of the CIA.

The addition of the intelligence aspect "effectively meant that JSOC was free to act as a spy agency and kill/capture force rolled into one," Scahill writes.

JSOC even ran an interrogation program, parallel to the CIA's black sites, that would provide the administration with even more flexibility and less oversight (See: Camp Nama).

Rumsfeld worked to make sure that the unit was "unrestrained and unaccountable to anyone except him, Cheney, and the president" while Cheney began going to JSOC headquarters at Fort Bragg in North Carolina to give direct action orders.

"It grew and went out of control under the vice president. It kinda went wild," Vincent Cannistraro, a career CIA counterterrorism officer, told Scahill. "There were a couple of places where, because they weren't coordinated, they weren't informed, they killed people that were not real targets. They were wrong. It happened, frequently."

In September 2003 JSOC, led by Gen. Stanley McChrystal, was running the show in Iraq, including training Iraqi Special Ops units that became unaccountable death squads.
It was also making its presence known in Afghanistan.

Lt. Col. Anthony Shaffer (Ret.), a career military intelligence officer who wrote the book "Operation Dark Heart," wrote that JSOC's force in Afghanistan "had the best technology, the best weapons, the best people — and plenty of money to burn."

From "Dirty Wars":

Unlike the Green Berets, JSOC was not in the country to win any hearts and minds. Once JSOC took charge, the mission would no longer resemble anthropology. It was to be a manhunt, at times an assassination machine.

In early 2004 Rumsfeld signed a secret order, known as the Al Qaeda Network Execute Order, that "streamlined JSOC's ability to conduct operations and hit targets outside of the stated battlefields of Iraq and Afghanistan."
By mid-2004 JSOC operations in Iraq had accelerated dramatically to the point where they were effectively "running the covert war buried within the larger war and controlling the intelligence," Scahill writes.

In 2005 and 2006 JSOC had its hands full with the Iraqi insurgency. It recruited 12 "tactical action operatives" from the private military company Blackwater from a secret raid (code-named Operation Fury) targeting an al Qaeda facility inside Pakistan.

Scahill notes that by 2007 the budget for U.S. special operations had grown to more than $8 billion annually, up 60 percent from 2003.

In January 2007, Scahill writes, JSOC began "a concentrated campaign of targeted assassinations and snatch operations" in Somalia while a CIA-backed Ethiopian force began an ill-fated invasion of the country.

In June 2008 Vice Admiral William McRaven took charge of JSOC, and the next month President Bush approved a secret order authorizing Special Ops Forces (as opposed to their Blackwater contractors) to conduct strikes in Pakistan without the country's permission.

Special Operations Forces were now being used to "go in and capture or kill people who were supposedly linked to extremist organizations around the world, in some cases allied countries," a source dubbed "Hunter," an operator who worked with JSOC on acknowledged and unacknowledged battlefields, told Scahill.

From "Dirty Wars":

The mindset, [Hunter] said, was, "The world is a battlefield and we are at war. Therefore the military can go wherever they please and do whatever it is that they want to do, in order to achieve the national security objectives of whichever administration happens to be in power."
 
Shortly after Barack Obama took office in January 2009, Scahill writes, he gave "carte blanche to JSOC and the CIA to wage a global manhunt. Capture was option two."