“Who the fuck did that?” The words greeting the first-ever combat strike by a remotely piloted aircraft were uttered not in praise but in anger. A botched Hellfire-missile attack by a CIA Predator had just cost the United States a likely chance to kill Taliban Supreme Commander Mullah Mohammed Omar. In response, the U.S. Air Force general in charge of airstrikes in Afghanistan was about to threaten to call off the entire opening campaign of the War on Terror, unless he was given control of the CIA’s secret weapon.

It was the night of October 7, 2001, less than a month after 9/11, and from the United States’ new Combined Air Operations Center (CAOC) in Saudi Arabia, it was the job of Lieutenant General Chuck Wald and his deputy Dave Deptula to coordinate every aspect of the unfolding Afghan air war. Operation Enduring Freedom—the campaign to rid Afghanistan of al-Qaeda and its Taliban hosts—was the first offensive of a global conflict that would eventually consume many tens of thousands of lives and trillions of dollars, and see more than two and a half million U.S. personnel sent into battle.

In the autumn of 2001, however, the United States was unwilling to launch a full-scale land invasion in a region 7,000 miles from home. Instead, a plan evolved to send into Afghanistan a small number of CIA agents and Special Forces in support of anti-Taliban militias, with the aid of the U.S. Air Force. That first October night was a powerful display of coordination involving laser-guided munitions dropped from the air and Tomahawk cruise missiles launched from the sea. General Tommy Franks, who then led the U.S. Central Command (CENTCOM), the military command overseeing operations in Afghanistan, wrote in his memoir American Soldier that the assault involved in total some 40,000 personnel, 393 aircraft, and 32 ships.

But one aircraft did not feature at all in the Air Force’s complex planning: a tiny, CIA-controlled, propeller-driven spy plane, which had crept into Afghanistan some hours earlier. Predator tailfin number 3034 now hangs suspended in the Smithsonian Air and Space Museum in Washington, D.C., its place in history assured. Yet its actions that first night of the war—in which numerous agencies in the vast U.S. military-intelligence machine each played sharply contradictory roles—remain steeped in controversy.

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The southern city of Kandahar was the epicenter of Taliban power in Afghanistan. U.S. intelligence officials had identified the home of Mullah Omar in the city and were watching unseen from a CIA Predator drone as a convoy of vehicles left the building complex. “We observed Mullah Omar, or 98-percent probable it was he, coming out of his facility in an entourage,” Deptula told me in an interview. When Omar stopped and entered another building complex, the United States had an opportunity to deliver a devastating blow to its enemies in the opening minutes of the war.

But there was a problem. There had never been a lethal action by a remotely piloted aircraft before, and the rules governing the operation of the Predator were blurred and untested. Air Force operators overseen by CIA analysts were piloting the Predator over Kandahar from the grounds of the agency’s headquarters in Langley, Virginia. According to Franks’s memoir, though, CENTCOM—not the CIA or the Air Force—had the final say on who would pull the trigger. At the same time, Air Force personnel at the sophisticated CAOC in Saudi Arabia were supposedly in charge of the entire air campaign. According to Deptula, the CAOC already had F-16 fighter aircraft on standby 20 miles to the south, armed with 1,000-pound bombs. “We wanted to use those weapons against the facility where Mullah Omar and his senior Taliban staff were hiding,” he told me.

But CENTCOM and the CIA had decided instead to use the untested Predator. Wald said he and Deptula were kept completely out of the loop on what happened next, “whether out of malice or incompetence I still don’t know. ... The first I knew the Predator was [engaged] was when I heard an unknown voice on my radio say, ‘You are cleared to fire.’” Instead of striking Omar’s facility, the Predator targeted and destroyed a vehicle outside, killing several bodyguards. In the chaotic moments that followed, the Taliban leader escaped. “Mullah Omar and his senior staff piled out of that building and here we are 13 years later and we don’t know where he is,” said Deptula. He is still angry about the failed opportunity. “What was the rationale of shooting an empty truck when the leadership was in an adjacent building, and where we had, two minutes away, aircraft that could have sent Mullah Omar and the senior Taliban leadership to the nether regions? It was a significant lost strategic opportunity—to put it mildly.”

The botched Predator strike led to an immediate three-way fight between the Air Force, CENTCOM, and the CIA, which risked bringing the first night of the War on Terror to a shuddering halt. “To this day,” Deptula said, “there is a degree of uncertainty over just who issued that fire order. We both watched the weapon impact and both turned to each other simultaneously and said, ‘Who the fuck did that?’” So furious was Wald that he threatened to call off the first night’s bombings. As Deptula conceded to me, in the rush to go to war “there had not been a lot of attention paid” to working out who was in charge of the drone. Tommy Franks has put it more bluntly: “In combat there has to be one line of authority. But in this goat rope there had been CENTCOM, the Pentagon, the White House, [and] the CIA.”

The regular Air Force and U.S. Special Forces got their own armed drone fleets after 2001. Yet tensions persist even now between the military, the intelligence community, and the White House over where control of America’s secret drone killings in Yemen, Somalia, and Pakistan—outside of declared U.S. war zones—should lie.

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It was a pair of Colorado-born brothers, James Neal and Linden Blue, now in their late 70s, who put the world’s first armed drone into production. Their business acumen was clear even in 1957, when they hatched a plan to learn to fly and convinced Life magazine to sponsor them for $8,000 on a South American adventure, flying in a tiny borrowed Tri-Pacer plane they nicknamed “Blue Bird.” The brothers made the cover that April, two all-American boys squashed into a tiny cockpit under the headline “Great Adventures: Over Andes by Light Plane.” The extraordinary trip took them 25,000 miles in 110 days through much of South America.

After leaving university, the pair first tried their hand at farming in Nicaragua. They had met and interviewed the late father of the country’s president and dictator Luis Somoza Debayle on their Life trip. Now, in a reported joint venture with Somoza’s family, the Blue brothers set up a ranch—complete with airstrip—on Nicaragua’s Caribbean coast, with the aim of cultivating cocoa and bananas. The project was a failure, the bananas blighted by disease. But their ties to the Somoza family proved important to their later ventures.

In 1986, the duo bought nuclear and defense contractor General Atomics from Chevron for a knock-down $50 million. By then, the Blue brothers had diverse business interests including real estate, construction, ranching, and gas, and they were keen to expand their energy interests. But there was also a more personal agenda. Their friends the Somozas had been deposed by the revolutionary Sandinistas in 1979, and the Reagan administration had authorized the CIA to assist a secret war against Nicaragua’s new leaders. The Blues were keen to help, since “the Contras were resisting communism and the domination of the Soviet Union,” as Linden put it in an interview with the journalist Di Freeze. As Neal told Charles Duhigg of The New York Times, the brothers were “enthusiastic supporters,” though not formally involved in the secret war.

It was Neal who began considering the possibility of using primitive unmanned aircraft on kamikaze missions against Nicaragua’s gasoline infrastructure: “You could launch them from behind the line of sight, so you would have total deniability,” he told Fortune magazine years later. The duo wanted to use their new General Atomics company to research the possibility. That early project went under the name “Predator,” though it was a dead end. It would be another six years before the Blue brothers snared the prototype of the armed drone that now bears that name, acquired from an Israeli-American design genius.

Abe Karem—“the  Moses of  modern drones,” as one senior Pentagon official described him to me—had served as an aeronautical engineer with the Israeli Air Force before running a team of radical innovators at state-owned Israel Aircraft Industries (still a world leader in drone design). In the wake of the Yom Kippur War in 1973, the country had “an emerging operational need for real-time intelligence on the front lines,” Karem told me via email. On leaving Israel Aircraft Industries, Karem set up his own company aimed at making unmanned aerial vehicle (UAV) systems. Unable to break into Israel’s close-knit defense world, he instead moved his family and business to California, where he built early models of his new drone designs in his three-car Los Angeles garage.

Those designs soon caught the attention of the CIA and the Pentagon. In 1983, nearly 300 U.S. and French peacekeepers had died in Beirut in terrorist attacks, starkly highlighting the need to keep closer tabs on radicals in areas like Lebanon’s Bekaa Valley. Yet such places were difficult to access and harder still to insert human spies into. Satellites and U-2 reconnaissance planes could provide photographs at specific times, but the process was cumbersome and technically limited. What was needed was an unobtrusive aircraft that could fly at lower altitude, loiter at the scene unobserved, and then quickly deliver pictures. Karem’s Leading Systems was contracted as part of a $40-million “black ” Pentagon project to develop its UAV technology.

What no one gave any thought to at the time was arming such a platform. Major General George Harrison, the former head of the Air Force’s Operational Test and Evaluation Center, recalled in an interview that there was huge institutional opposition at the Pentagon and CIA to the idea of arming any surveillance aircraft: “[I]f you were armed it would divert you from your primary job of target development. So there was strong resistance, I mean strong resistance, I can’t overstate it.”

Karem’s two prototypes, the Amber and the Gnat, first successfully flew in 1986. Four years later, Leading Systems was bankrupt—the Pentagon had frozen its funding as a result of inter-services bickering and post‒Cold War cuts. In a particular irony, Pakistan at one point considered buying the mothballed prototype fleet. But in 1991, the Blue brothers happened to be looking for a UAV company to buy, and Karem’s was it. The Predator was back in business.

The Predator in 1998 (Reuters / Jeffrey S. Viano-U.S. Navy)

When Bill Clinton assumed the U.S. presidency in January 1993, a key priority was the escalating conflict across the former Yugoslavia. A lack of good intelligence, surveillance, and reconnaissance was hampering U.S. efforts to understand and, if possible, contain the civil wars. The CIA wanted spies in the sky, and agency director James Woolsey played an important role in the Predator’s early success. Briefed about the drone’s potential at an early 1993 meeting—and concerned about the quality of satellite coverage over the Balkans—the CIA chief is said to have personally flown to California to inspect the new system. Impressed, the agency bought five Gnats on the spot. It also brought into play its own expertise stemming from research it had done on how to remotely pilot an aircraft from thousands of miles away. CIA know-how now merged with General Atomics’ expertise.

In record time, General Atomics’ prototypes were approved for deployment in the escalating Balkan Wars. Though the Pentagon had also ordered drones from General Atomics, just as with the War on Terror seven years later, the CIA’s drones got there first. The agency flew its classified Bosnian missions from the semi-derelict Gjader airfield in Albania. A year later, the Pentagon’s own drones arrived in the shape of four modified Gnats (newly christened “Predators”), which operated from Taszar airfield in Hungary and which were controlled by the U.S. military.

The early Predator had major limitations, many of which were ironed out in a literal trial by combat since they were easy prey for Serbian anti-air defenses. At least two were shot down. Wings would also freeze up, sometimes causing a drone to drop expensively from the sky. Missing too was the facility to fly the remotely piloted aircraft from any distance via satellites. Instead, the pilots, sensor operators, and intelligence analysts were all crammed into huts beside the runways. Yet with its ability to stay in the air for almost 24 hours, the Predator was still proving an effective reconnaissance machine. “The bad guys used to just wait for our fighter pilots to leave,” recalled Air Force Major General Ken Israel, who headed the Pentagon office in charge of unmanned military aircraft at the time. “They didn’t have that option anymore.”

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It was Osama bin Laden who provided the catalyst for arming the drone. In August 1998, coordinated suicide bombings occurred at two U.S. embassies 400 miles apart in Nairobi, Kenya and Dar-es-Salaam, Tanzania. The FBI later concluded that the attack had been sponsored by bin Laden and his deputy Ayman al-Zawahiri. But if the United States wanted to deal with bin Laden directly, it first had to find him. For a time, the Pentagon considered placing a giant, hidden telescope on an Afghan mountain in the hope of spotting al-Qaeda’s gaunt leader. More sensible heads turned to the Predator, which could not only help find him, but could laser-illuminate his location so Tomahawk cruise missiles could be launched from a submarine in the Gulf.

On September 7, 2000, the first unarmed, remotely piloted aircraft crossed into Afghanistan. Over the next few weeks, the Predator made 10 successful flights into the country, and on September 25, 2000, against all expectations, it apparently found bin Laden. Circling high and unseen above Tarnak Farms near Kandahar, the Predator fed back live pictures of a tall, white-robed man surrounded by a security detail. According to one senior Pentagon official with close knowledge of the operation, in total al-Qaeda’s leader was directly observed by the CIA’s drones for four hours and 23 minutes over a number of missions.

Yet there was no guarantee that cruise missiles would find the terrorist in the same location by the time orders were issued, coordinates were inputted and checked, lawyers were consulted, and the missile made its way from the Gulf to the target. An armed Predator, on the other hand, could have spotted and killed bin Laden at the same time. “We showed that [bin Laden] video to the secretary of the Air Force, the chief of staff of the Air Force and the assistant vice chief and someone mentioned, ‘Let me take Hellfire’”—a lightweight anti-tank missile that could be laser-guided onto its target—“‘quick, black, and dirty.’ That direction was given, so we moved money and notified Congress.” The CIA had developed the Predator as a spying platform. Now the rush was on to turn it into an assassination tool.

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General Atomics’ newly armed drone was still being tested and evaluated in the fall of 2001 when, following the terrorist attacks of September 11, it was called into service early by the CIA, crated up, and shipped off to the impending war in Afghanistan. Its capabilities and shortcomings would be determined in the heat of battle. It was a shaky start. On October 12—just five days after the Mullah Omar incident—a CIA forward team was almost bombed by an agency drone after analysts apparently mistook its members for al-Qaeda, according to the memoirs of former CIA officer Gary Schroen.

By mid-November 2001, the CIA’s drones had reportedly fired 40 Hellfire missiles throughout Afghanistan, although this should be measured against an estimated 6,500 airstrikes by all platforms during the three-month air war. By December 2001, President George W. Bush would himself come out strongly as a Predator fan in an address to cadets at The Citadel, The Military College of South Carolina. Describing what was still a secret CIA weapon, he spoke of how drones were now “able to circle over enemy forces, gather intelligence, transmit information instantly back to commanders, then fire on targets with extreme accuracy.” Bush boasted that “the conflict in Afghanistan has taught us more about the future of our military than a decade of blue-ribbon panels and think-tank symposiums.” The armed Predator had made a powerful debut on the modern battlefield.

Fourteen years and hundreds of targeted assassinations later, military leaders still grate at a civilian intelligence agency with its own lethal drone air force. Yet every Pentagon effort to seize control of the program has failed. The CIA has become expert at killing in secret from the air, at the behest of the president, and neither Bush nor Obama have seen fit to relinquish that power.

This article has been excerpted from Chris Woods’s new book, Sudden Justice: America’s Secret Drone Wars.