The headquarters for the American military's air war in Central Asia and the Middle East is located in a converted medical warehouse on an undisclosed base in a country the U.S. Air Force would rather not name. The lights are turned down low, so the troops can clearly see the giant screen at the far end of the in this cavernous, classified facility.

On that glowing screen is a digital map of Afghanistan, showing the position of every U.S. Air Force drone, every fighter jet, every bomber and every tanker aircraft with a teal dot. Most of the dots are positioned near the hotspots of the Afghanistan war – places like Kandahar, Helmand and Nangarhar provinces. But there are three dots, representing Air Force unmanned aerial vehicles, that aren't above Afghanistan at all. These dots have moved to the east of the Afghan border; these drones are flying missions over Pakistan.

Over the past year and a half, the United States has stepped up drone strikes against militants in Pakistan – killing as many as a thousand people, by some estimates. Press accounts have largely credited the Central Intelligence Agency with running these missions. Government officials have refused to speak in public about drone attacks, just as they routinely rebuff any attempt to probe into the CIA's operations. "I'm not going to comment on any particular tactic or technology," Secretary of State Hillary Clinton recently told a group of Pakistani journalists.

But the U.S. Air Force also plays an important role in the drone missions over Pakistan, according to current and former American military officials, and judging from what I saw at that undisclosed location. The military supplies the aircraft. It monitors the flights in and out of Pakistan. And, on occasion, Air Force pilots remotely fly their own drone missions over Pakistan. On that digital map are the far end of the warehouse, there's a note reminding troops exactly how much notice they must give before U.S. military planes enter Pakistani airspace.

U.S. military drones began flying over Pakistan soon after the invasion of Afghanistan in 2001. "I dealt with the Pakistani air chief from the beginning," says a former senior military officer. "At times, we operated a bit out of Pakistan."

Today, those missions have become a regular occurrence. The U.S. Air Force has a fleet of Predator and heavily-armed Reaper drones, stationed at Kandahar and Jalalabad Air Fields in Afghanistan. All of these robotic aircraft are allowed to venture occasionally into Pakistani airspace to pursue militants. The government in Islamabad just has to be notified first. Some of the Predators also fly into Pakistan on operations in conjunction with or in support of Islamabad's military.

These missions are remotely flown by U.S. Air Force pilots at Creech Air Force Base, Nevada; the footage is shared with the Pakistani government, including at joint coordination centers on the border.

In addition, some of the Predators and Reapers are placed under the operational control of the CIA, which uses them to conduct their own strike and surveillance missions. Some of those drones take off from Jalalabad, others from within Pakistan itself, at a remote base called Shamshi. According to the New York Times, those aircraft are operated out of CIA headquarters in Langley, Virginia.

The private security firm Blackwater, now known as "Xe," provides local security for the robotic aircraft, and helps assemble the drones' arrays of Hellfire missiles and 500-pound bombs. Those munitions are then unleashed during strikes on suspected militants, targeted by a combination of informants' tips, radio intercepts and overhead surveillance. Al Qaeda claims that cheap, battery-sized infrared beacons are handed out to local agents, who then use them to signal for drones to attack.

From what I can tell, these CIA missions comprise the bulk of the drone flights over Pakistan. And the military has, at times, encouraged the notion that operating the unmanned aircraft was the spy agency's job. "The overwhelming bulk of all activity in Afghanistan since the first U.S. forces went in have been basically under the control of the Central Command," then-Defense Secretary Donald Rumsfeld told reporters in 2002. "An exception has been the armed Predators, which are CIA-operated."

But while the CIA's drone flights are kept largely compartmentalized from the U.S. military's efforts in Afghanistan, there is overlap between the two. The Air Force has a total of 39 "orbits," or air patrols, currently operating in Central Asia and the Middle East. The CIA draws its Predators and Reapers from this pool of military drones. "There are 39 orbits, that's it. No wink, wink," a military officer says.

No matter who controls the mission, some airmen at the undisclosed base's warehouse-turned-war-room are aware of every flight, at least in general terms. The officers there at the Combined Air & Space Operations Center, or CAOC, need to have a basic idea of where every aircraft is, to keep them from crashing into one another in mid-air. That's simple air traffic control, just like in the civilian world.

Because the drones can fire missiles and bombs from miles away, there needs to be an added layer of monitoring. "You have to know where every bomb went, and where every bomb is supposed to go," a former senior military official says. "No one is just gonna allow the expenditure of ordnance out of the wild blue yonder." It's one of the many ways in which the air wars in Afghanistan and Pakistan are linked.

Ironically, these two connected air campaigns are almost mirror images of one another. On one side of the border, there's an influx of tens of thousands of U.S. troops; on the other, American boots on the ground have been largely forbidden, except for a handful of trainers from special forces. So instead, America uses a fleet of robotic aircraft, to avoid the prohibition against flesh-and-blood troops.

In Afghanistan, airstrikes have been strictly limited, to minimize casualties. In Pakistan – if news accounts about those assaults are even remotely accurate – the attacks are far, far more deadly. According to an analysis of public reports by the New America Foundation, 82 U.S. drone attacks in Pakistan since 2006 "have killed between 750 and 1,000 people." Up to 320 of those may have been civilians. The Long War Journal, examining the same records, calculates that 447 people have been killed in 42 reported drone strikes during the first nine months of 2009. The website estimates that only 10 percent of those deaths have been innocents.

But since the Pakistani government bans reporters and aid organizations from the tribal lands, where the majority of drone strikes have been reported, no one can say for sure how many have really been killed by the unmanned attackers.

The drone strikes in Pakistan have been widely credited with taking out senior leaders of both the Pakistani Taliban and Al Qaeda. But they've also come under increasing criticism, as a secret extension of the war in Central Asia fought under uncertain authority and with questionable morality.

It wasn't long ago that the United States condemned Israel for its "targeted killings" of Palestinian terrorists. Now, the U.S. pursues a similar tactic in its campaign against Al Qaeda. "The things we were complaining about from Israel a few years ago we now embrace," Georgetown University Law Center professor Gary Solis recently told the New Yorker. A week before the 9/11 attacks, then-CIA chief George Tenet argued that it would be "a terrible mistake" for "the Director of Central Intelligence to fire a weapon" like the Predator. Seven years later, current CIA director Leon Panetta says the drones are "the only game in town in terms of confronting or trying to disrupt the Al Qaeda leadership."

Recently, President Obama authorized a widening of the drone war in Pakistan. "Even more operations targeting terrorism safe havens," one American official tells the New York Times. "More people, more places, more operations."

It's not clear if the U.S. military will join the CIA in this expanded campaign.

Photo: Noah Shachtman

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