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A group of men who had just finished breakfast scrambled to get to their trucks. One was Anwar al-Awlaki, the firebrand preacher, born in New Mexico, who had evolved from a peddler of Internet hatred to a senior operative in Al Qaeda's branch in Yemen. Another was Samir Khan, another American citizen who had moved to Yemen from North Carolina and was the creative force behind Inspire, the militant group's English-language Internet magazine.

Two of the Predator drones pointed lasers on the trucks to pinpoint the targets, while the larger Reapers took aim. The Reaper pilots, operating their planes from thousands of miles away, readied for the missile shots, and fired.

It was the culmination of years of painstaking intelligence work, intense deliberation by lawyers working for President Obama and turf fights between the Pentagon and the C.I.A., whose parallel drone wars converged on the killing grounds of Yemen. For what was apparently the first time since the Civil War, the United States government had carried out the deliberate killing of an American citizen as a wartime enemy and without a trial.

Eighteen months later, despite the Obama administration's effort to keep it cloaked in secrecy, the decision to hunt and kill Mr. Awlaki has become the subject of new public scrutiny and debate, touched off by the nomination of John O. Brennan, Mr. Obama's counterterrorism adviser, to be head of the C.I.A.

The leak last month of an unclassified Justice Department "white paper" summarizing the administration's abstract legal arguments — prepared months after the Awlaki and Khan killings amid an internal debate over how much to disclose — has ignited demands for even greater transparency, culminating last week in a 13-hour Senate filibuster that temporarily delayed Mr. Brennan's confirmation. Some wondered aloud: If the president can order the assassination of Americans overseas, based on secret intelligence, what are the limits to his power?

This account of what led to the Awlaki strike, based on interviews with three dozen current and former legal and counterterrorism officials and outside experts, fills in new details of the legal, intelligence and military challenges faced by the Obama administration in what proved to be a landmark episode in American history and law. It highlights the perils of a war conducted behind a classified veil, relying on missile strikes rarely acknowledged by the American government and complex legal justifications drafted for only a small group of officials to read.

The missile strike on Sept. 30, 2011, that killed Mr. Awlaki — a terrorist leader whose death lawyers in the Obama administration believed to be justifiable — also killed Mr. Khan, though officials had judged he was not a significant enough threat to warrant being specifically targeted. The next month, another drone strike mistakenly killed Mr. Awlaki's 16-year-old son, Abdulrahman, who had set off into the Yemeni desert in search of his father. Within just two weeks, the American government had killed three of its own citizens in Yemen. Only one had been killed on purpose.

An Evolving Threat

By the time the missile found him, Mr. Awlaki, 40, had been under the scrutiny of American officials for more than a decade. He first came under F.B.I. investigation in 1999 because of associations with militants and was questioned after the 2001 terrorist attacks about his contacts with three of the hijackers at his mosques in San Diego and Virginia. But at other times, presenting himself as a moderate bridge-builder, he gave interviews to the national news media, preached at the Capitol in Washington and attended a breakfast with Pentagon officials.

In 2002, after leaving the United States for good, he endorsed the notion that the land of his birth was at war with Islam. In London, and then in Yemen, where he was imprisoned for 18 months with American encouragement, Mr. Awlaki inched steadily closer to a full embrace of terrorist violence. His eloquent, English-language exhortations to jihad turned up repeatedly on the computers of young plotters of violence arrested in Britain, Canada and the United States.

By 2008, said Philip Mudd, then a top F.B.I. counterterrorism official, Mr. Awlaki "was cropping up as a radicalizer — not in just a few investigations, but in what seemed to be every investigation."

In November 2009, when Maj. Nidal Malik Hasan, an Army psychiatrist, was charged with opening fire at Fort Hood in Texas and killing 13 people, Mr. Awlaki finally found the global fame he had long appeared to court. Investigators quickly discovered that the major had exchanged e-mails with Mr. Awlaki, though the cleric's replies had been cautious and noncommittal. But four days after the shootings, the cleric removed any doubt about where he stood.

"Nidal Hassan is a hero," he wrote on his widely read blog. "He is a man of conscience who could not bear living the contradiction of being a Muslim and serving in an army that is fighting against his own people."

As chilling as the message was, it was still speech protected by the First Amendment. American intelligence agencies intensified their focus on Mr. Awlaki, intercepting communications that showed the cleric's growing clout in Al Qaeda in the Arabian Peninsula, a Yemen-based affiliate of Osama bin Laden's terrorist network.

On Dec. 24, 2009, in the second American strike in Yemen in eight days, missiles hit a meeting of leaders of the affiliate group. News accounts said one target was Mr. Awlaki, who was falsely reported to have been killed.

In fact, other top officials of the group were the strike's specific targets, and Mr. Awlaki's death would have been collateral damage — legally defensible as a death incidental to the military aim. As dangerous as Mr. Awlaki seemed, he was proved to be only an inciter; counterterrorism analysts did not yet have incontrovertible evidence that he was, in their language, "operational."

That would soon change. The next day, a 23-year-old Nigerian named Umar Farouk Abdulmutallab tried and failed to blow up an airliner as it approached Detroit. The would-be underwear bomber told F.B.I. agents that after he went to Yemen and tracked down Mr. Awlaki, his online hero, the cleric had discussed "martyrdom and jihad" with him, approved him for a suicide mission, helped him prepare a martyrdom video and directed him to detonate his bomb over United States territory, according to court documents.

In his initial 50-minute interrogation on Dec. 25, 2009, before he stopped speaking for a month, Mr. Abdulmutallab said he had been sent by a terrorist named Abu Tarek, although intelligence agencies quickly found indications that Mr. Awlaki was probably involved. When Mr. Abdulmutallab resumed cooperating with interrogators in late January, an official said, he admitted that "Abu Tarek" was Mr. Awlaki. With the Nigerian's statements, American officials had witness confirmation that Mr. Awlaki was clearly a direct plotter, no longer just a dangerous propagandist.

"He had been on the radar all along, but it was Abdulmutallab's testimony that really sealed it in my mind that this guy was dangerous and that we needed to go after him," said Dennis C. Blair, then director of national intelligence.

A Legal Quandary

David Barron and Martin Lederman had a problem. As lawyers in the Justice Department's Office of Legal Counsel, it had fallen to them to declare whether deliberately killing Mr. Awlaki, despite his citizenship, would be lawful, assuming it was not feasible to capture him. The question raised a complex tangle of potential obstacles under both international and domestic law, and Mr. Awlaki might be located at any moment.

According to officials familiar with the deliberations, the lawyers threw themselves into the project and swiftly completed a short memorandum. It preliminarily concluded, based on the evidence available at the time, that Mr. Awlaki was a lawful target because he was participating in the war with Al Qaeda and also because he was a specific threat to the country. The overlapping reasoning justified a strike either by the Pentagon, which generally operated within the Congressional authorization to use military force against Al Qaeda, or by the C.I.A., a civilian agency which generally operated within a "national self-defense" framework deriving from a president's security powers.

They also analyzed other bodies of law to see whether they would render a strike impermissible, concluding that they did not. For example, the Yemeni government had granted permission for airstrikes on its soil as long as the United States did not acknowledge its role, so such strikes would not violate Yemeni sovereignty.

And while the Constitution generally requires judicial process before the government may kill an American, the Supreme Court has held that in some contexts — like when the police, in order to protect innocent bystanders, ram a car to stop a high-speed chase — no prior permission from a judge is necessary; the lawyers concluded that the wartime threat posed by Mr. Awlaki qualified as such a context, and so his constitutional rights did not bar the government from killing him without a trial.

But as months passed, Mr. Barron and Mr. Lederman grew uneasy. They told colleagues there were issues they had not adequately addressed, particularly after reading a legal blog that focused on a statute that bars Americans from killing other Americans overseas. In light of the gravity of the question and with more time, they began drafting a second, more comprehensive memo, expanding and refining their legal analysis and, in an unusual step, researching and citing dense thickets of intelligence reports supporting the premise that Mr. Awlaki was plotting attacks.

Their labors played out against the backdrop of how some of their predecessors under President George W. Bush had become defined by their once-secret memos asserting a nearly unlimited view of executive authority, like that a president's wartime powers allowed him to defy Congressional statutes limiting torture and surveillance.

Indeed, Mr. Barron and Mr. Lederman had produced a definitive denunciation of such reasoning, co-writing a book-length, two-part Harvard Law Review essay in 2008 concluding that the Bush team's theory of presidential powers that could not be checked by Congress was "an even more radical attempt to remake the constitutional law of war powers than is often recognized." Then a senator, Mr. Obama had called the Bush theory that a president could bypass a statute requiring warrants for surveillance "illegal and unconstitutional."

Now, Mr. Barron and Mr. Lederman were being asked whether President Obama's counterterrorism team could take its own extraordinary step, notwithstanding potential obstacles like the overseas-murder statute. Enacted as part of a 1994 crime bill, it makes no exception on its face for national security threats. By contrast, the main statute banning murder in ordinary, domestic contexts is far more nuanced and covers only "unlawful" killings.

As they researched the rarely invoked overseas-murder statute, Mr. Barron and Mr. Lederman discovered a 1997 district court decision involving a woman who was charged with killing her child in Japan. A judge ruled that the terse overseas-killing law must be interpreted as incorporating the exceptions of its domestic-murder counterpart, writing, "Congress did not intend to criminalize justifiable or excusable killings."

And by arguing that it is not unlawful "murder" when the government kills an enemy leader in war or national self-defense, Mr. Barron and Mr. Lederman concluded that the foreign-killing statute would not impede a strike. They had not resorted to the Bush-style theories they had once denounced of sweeping presidential war powers to disregard Congressionally imposed limitations.

Due to return to academia in the fall of 2010, the two lawyers finished their second Awlaki memorandum, whose reasoning was widely approved by other administration lawyers, that summer. It had ballooned to about 63 pages but remained narrowly tailored to Mr. Awlaki's circumstances, blessing lethal force against him without addressing whether it would also be permissible to kill citizens, like low-ranking members of Al Qaeda, in other situations.

Nearly three years later, a version of the legal analysis portions would become public in the "white paper," which stripped out all references to Mr. Awlaki while retaining echoes, like its discussion of a generic "senior operational leader." Divorced from its original context and misunderstood as a general statement about the scope and limits of the government's authority to kill citizens, the free-floating reasoning would lead to widespread confusion.

Heightening Intelligence

Now the lawyers had twice signed off on killing Mr. Awlaki if he could not be captured — but the government still had no idea where in Yemen he was hiding. During the first half of 2010 the C.I.A. was just ramping up intelligence gathering in the country, and Saudi spies had yet to penetrate militant networks in Yemen deeply enough to learn the whereabouts of leaders of Al Qaeda in the Arabian Peninsula.

Mr. Awlaki appears to have hidden most of the time in Shabwa Province, several hours' drive southeast of the capital, turf for Al Qaeda and also the traditional territory of his family's powerful tribe, the Awaliq. Yemen's cagey longtime president, Ali Abdullah Saleh, negotiated with tribal leaders, who offered to hold Mr. Awlaki under house arrest, according to a Yemeni official. The talks were inconclusive.

And there were other problems. A disastrous American missile strike in May 2010 accidentally killed a deputy provincial governor in Yemen and infuriated President Saleh, effectively suspending the clandestine war. It would be months before the Pentagon's next strike in Yemen.

In August 2010, Mr. Awlaki's father, with help from civil liberties groups, filed a lawsuit in Washington challenging the government plan to kill his son, which had been reported in the news media. In court filings, the administration marshaled its public claims against Mr. Awlaki and said he could always surrender.

But it also declared that courts should play no role in overseeing the executive branch's wartime targeting decisions, argued that Mr. Awlaki's father had no legal standing to bring the case, and invoked the state secrets privilege. In December 2010, a judge dismissed the suit.

Back in Yemen, the C.I.A. and the Pentagon used the pause in the air campaign to develop more sources inside the country. The National Security Agency stepped up monitoring of cellphones in Yemen and penetrated computer networks to intercept electronic messages. Aware that Mr. Obama, shaken by the underwear bombing attempt, was closely following the hunt, agencies competed to get new scraps about Mr. Awlaki into the president's daily intelligence briefing, a former Defense Intelligence Agency analyst said.

And, very quietly, the C.I.A. began to build its own drone base in Saudi Arabia. Saudi officials had given the C.I.A. permission to build the base on the condition that the kingdom's role was masked. And the base took care of a separate problem: the government of Djibouti, where the military was basing its drone operations in the region, put tight restrictions on any lethal operations carried out from its soil. The Saudi government made no similar demands.

Meanwhile, attacks linked in various ways to Mr. Awlaki continued to mount, including the attempted car bombing of Times Square in May 2010 by Faisal Shahzad, a naturalized American citizen who had reached out to the preacher on the Internet, and the attempted bombing by Al Qaeda in the Arabian Peninsula of cargo planes bound for the United States that October.

In late 2010 or early 2011, Yemeni security troops surrounded a village in Shabwa Province where Mr. Awlaki was reported to be hiding, said Gregory Johnsen, a Princeton scholar and author of "The Last Refuge: Yemen, al-Qaeda, and America's War in Arabia." But a house-to-house search did not find him.

At the White House, frustration was mounting.

The Hunt Narrows

Even as the hunt went on, Yemen's strongman began to lose his grip on power as his country was caught up in the revolts sweeping the Arab world in early 2011.

That June, a barrage of rockets struck the room of the presidential palace where Mr. Saleh was hiding, severely injuring him and effectively ending his rule.

The weakening of Mr. Saleh gave the Americans more latitude for the Awlaki manhunt. By then, American and Saudi spies had turned a number of militants into sources, helping to guide American strikes.

In its most exotic effort to track the cleric, the C.I.A. worked with Danish intelligence to use Morten Storm, a Danish convert who had befriended Mr. Awlaki, to put a tracking device on the suitcase of a woman who had agreed to become the cleric's third wife. The plan failed when Mr. Awlaki's wary associates discarded the suitcase. But Mr. Storm also told the authorities that he communicated with Mr. Awlaki via a courier; it is not clear whether that courier eventually helped lead the C.I.A. to Mr. Awlaki's location.

Other sources of information were also emerging, and one led to a new debate. In April 2011, the United States captured Ahmed Abdulkadir Warsame, a Somali man who worked closely with the Qaeda affiliate in Yemen. He was held aboard a naval vessel for more than two months and spoke freely to interrogators, including about his encounters with the former North Carolina man now editing the group's magazine, Samir Khan.

While the United States had long tracked Mr. Khan, the new details from the Warsame interrogation raised the question of whether another American citizen should be considered for targeting. There was still scant evidence tying Mr. Khan to any specific plot, so the administration left him off the list. But events would not turn out so neatly.

In May 2011, days after the American commando raid in Pakistan that killed Bin Laden, the Pentagon's Joint Special Operations Command, the hub for classified Army and Navy commando units, had its best chance to kill Mr. Awlaki as he moved around Shabwa Province. Drones and Marine Harrier jets fired at his truck, but he managed to escape and took refuge in a cave. According to Mr. Johnsen, the Princeton expert, Mr. Awlaki told friends that the episode "increased my certainty that no human being will die until they complete their livelihood and appointed time."

Finally, by late September 2011, the C.I.A. base in Saudi Arabia was ready. Mr. Obama's counterterrorism adviser, Mr. Brennan, directed that lead responsibility for the Awlaki hunt would be shifted to the agency. David H. Petraeus, who had taken over as C.I.A. director on Sept. 6, ordered several drones to be relocated from Pakistan to Saudi Arabia. By mid-September, the Americans were closing in — with updates from a C.I.A. source inside Al Qaeda in the Arabian Peninsula, officials say. That was when a very different search for Mr. Awlaki began.

As Mr. Awlaki had become one of the world's most hunted terrorists, his 16-year-old son Abdulrahman had lived the life of a normal adolescent. He liked sports and music and kept his Facebook page regularly updated. But now he sneaked out of the family home in Sana, Yemen's capital, leaving an apologetic note for his mother saying that he had gone to find his father.

But by the time the teenager headed to Shabwa, his father had left for Jawf Province, hundreds of miles away. Accompanied by Mr. Khan, the elder Awlaki moved about the rugged territory, wary of staying anywhere for long.

What he did not know was that the C.I.A.'s source was reporting the movements. On the morning of Sept. 30, guided by the tipster, the fleet of drones arrived above Jawf. Missiles destroyed the convoy.

The same day, at a military ceremony at Fort Myer in Arlington, Va., Mr. Obama took note of the victory for the immense American counterterrorism effort — but in oddly indirect language. Mr. Awlaki, he said, "was killed" in Yemen, and "this success is a tribute to our intelligence community and to the efforts of Yemen and its security forces who have worked closely with the United States."

Mr. Obama had immediately declassified the Bin Laden raid. But this time he signaled that the operation in Yemen, though already reported around the globe, would remain officially unacknowledged. Members of Congress would speak only cautiously about it, and counterterrorism officials could discuss only privately what the whole world knew.

Administration officials who had labored for months to evaluate the killing of Mr. Awlaki took stock. Mr. Khan, whom they had specifically decided not to add to the kill list, was dead, too. While the lawyers believed that his killing was legally defensible as collateral damage, the death cast a cloud over all those months of seemingly cautious efforts to analyze who should go on the list and who should not.

Then, on Oct. 14, a missile apparently intended for an Egyptian Qaeda operative, Ibrahim al-Banna, hit a modest outdoor eating place in Shabwa. The intelligence was bad: Mr. Banna was not there, and among about a dozen men killed was the young Abdulrahman al-Awlaki, who had no connection to terrorism and would never have been deliberately targeted.

It was a tragic error and, for the Obama administration, a public relations disaster, further muddying the moral clarity of the previous strike on his father and fueling skepticism about American assertions of drones' surgical precision. The damage was only compounded when anonymous officials at first gave the younger Mr. Awlaki's age as 21, prompting his grieving family to make public his birth certificate.

He had been born in Denver, said the certificate from the Colorado health department. In the United States, at the time his government's missile killed him, the teenager would have just reached driving age.