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On Thursday, November 6, 2008, two days after he was elected president of the United States, Senator Barack Obama arranged to meet in Chicago with Mike McConnell, the director of national intelligence (DNI).

McConnell, 65, a retired Navy vice admiral with stooped shoulders, wisps of light brown hair and an impish smile, had come to present details of the most highly classified intelligence operations and capabilities of the vast American espionage establishment he oversaw as DNI. In just 75 days, the formidable powers of the state would reside with the 47-year-old Obama. He would soon be, as the intelligence world often called the president, “The First Customer.”

McConnell arrived early at the Kluczynski Federal Building, an austere Chicago skyscraper, with Michael J. Morell, who had been President George W. Bush’s presidential briefer on 9/11 and now headed the Central Intelligence Agency’s analysis division.

Two members of Senator Obama’s transition team from the last Democratic administration greeted them: John Podesta, Bill Clinton’s chief of staff for the final two years of his presidency, and James Steinberg, a former deputy national security adviser in the Clinton White House.

“We’re going to go in with the president-elect and hear what you guys have got to say,” Podesta said.

McConnell paused awkwardly. He had received instructions from President Bush. “As president,” Bush had told McConnell, “this is my decision. I forbid any information about our success and how this works” except to the president-elect. McConnell knew Bush had never been comfortable using the terminology “sources and methods.” But what the president meant was that nothing should be disclosed that might identify human spies and new techniques developed to infiltrate and attack al Qaeda, fight the wars in Iraq and Afghanistan, and defend the nation.

“John, sorry,” McConnell said. “I’d love to be able to accommodate, but I didn’t make these rules.” He related Bush’s instructions—only the president-elect and anyone designated to take a top national security cabinet post could attend. “Neither of you are designated. So I can’t. I’m not going to violate the president’s direction.”

“Okay, I got it,” Podesta said, barely concealing his irritation. Podesta had had all-source intelligence access before, as had Steinberg. He thought this was not helpful to Obama, who was largely unfamiliar with intelligence briefings.

Obama arrived still in full campaign mode with ready smiles and firm handshakes all around. He was buoyant in the afterglow of victory.

Two months earlier, after receiving a routine top secret briefing from McConnell on terrorism threats, Obama had half joked, “You know, I’ve been worried about losing this election. After talking to you guys, I’m worried about winning this election.”

“Mr. President-elect, we need to see you for a second,” Podesta said, steering him off to a private room. When Obama returned, his demeanor was different. He was more reserved, even aggravated. The transition from campaigning to governing—with all its frustrations—was delivering another surprise. His people, the inner circle from the campaign and the brain trust of Democrats he had carefully assembled to guide his transition, were being excluded. The first customer–elect was going to have to go it alone.

McConnell and Morell sat down with Obama in a private, secure room called a Sensitive Compartmented Information Facility, or SCIF. It was an unusually small room in the center of the building where a bathroom might normally be located. Designed to prevent eavesdropping, the SCIF was windowless and confining, even claustrophobic.

At first, this would be something of a continuation and amplification of the earlier briefing McConnell had given candidate Obama. There were 161,000 American troops at war in Iraq and 38,000 in Afghanistan. Intelligence was making significant contributions to the war efforts. But the immediate threat to the United States came not from these war zones, but from Pakistan, an unstable country with a population of about 170 million, a 1,500-mile border with southern Afghanistan, and an arsenal of some 100 nuclear weapons.

Priority one for the DNI, and now Obama, had to be the ungoverned tribal regions along the Pakistan-Afghanistan border where Osama bin Laden, his al Qaeda network, and branches of the extremist insurgent Taliban had nested in 150 training camps and other facilities.

Combined, the seven regions forming Pakistan’s Federally Administered Tribal Areas (FATA) were about the size of New Jersey. The extremist groups and tribal chiefs ruled much of the FATA and had footholds in Pakistan’s Northwest Frontier province.

In September 2006, Pakistan had signed a treaty ceding full control of the FATA’s North Waziristan region to Taliban-linked tribal chiefs, creating a kind of Wild West for al Qaeda and the Taliban insurgents attacking the U.S. forces in Afghanistan.

In the earlier briefing, McConnell had laid out the problem in dealing with Pakistan. It was a dishonest partner of the U.S. in the Afghanistan War. “They’re living a lie,” McConnell had said. In exchange for reimbursements of about $2 billion a year from the U.S., Pakistan’s powerful military and its spy agency, Inter-Services Intelligence (ISI), helped the U.S. while giving clandestine aid, weapons and money to the Afghan Taliban. They had an “office of hedging your bets,” McConnell said.

Dealing with the ISI would break your heart if you did it long enough, McConnell had explained. It was as if there were six or seven different personalities within the ISI. The CIA exploited and bought some, but at least one section—known as Directorate S—financed and nurtured the Taliban and other terrorist groups. CIA payments might put parts of the ISI in America’s pocket, McConnell had said, but the Pakistani spy agency could not or would not control its own people.

The Pakistani leadership believed the U.S. would eventually withdraw from the region, as it had toward the end of the Cold War once the occupying Soviet forces retreated from Afghanistan in 1989. Their paranoid mind-set was, in part, understandable. If America moved out again, India and Iran would fill the power vacuum inside Afghanistan. And most of all, Pakistan feared India, an avowed enemy for more than 60 years. As a growing economic and military powerhouse, India had numerous intelligence programs inside Afghanistan to spread its influence there. Pakistan worried more about being encircled by India than being undermined by extremists inside its borders.

The best way out of this would be for Obama to broker some kind of peace between India and Pakistan, the DNI had said. If Pakistan felt significantly more secure in its relations with India, it might stop playing its deadly game with the Taliban.

In his September overview, McConnell also discussed strikes by small unmanned aerial vehicles such as Predators that had sophisticated surveillance cameras and Hellfire missiles. The covert action program authorized by President Bush targeted al Qaeda leadership and other groups inside Pakistan. Although classified, the program had been widely reported in the Pakistani and American media.

Only four strikes had been launched in the first half of 2008, Obama had been told. The U.S. had uncovered evidence that the Pakistanis would delay planned strikes in order to warn al Qaeda and the Afghan Taliban, whose fighters would then disperse. In June 2008, McConnell had taken human and technical intelligence to President Bush showing multiple conversations between an ISI colonel and Siraj Haqqani, a guerrilla commander whose network was allied with the Afghan Taliban.

“Okay,” Bush had said, “we’re going to stop playing the game. These sons of bitches are killing Americans. I’ve had enough.” He ordered stepped-up Predator drone strikes on al Qaeda leaders and specific camps, so-called infrastructure targets. It was like attacking an anthill—the survivors would run away in the aftermath. These “squirters” were then tracked to the next hideout, helping to build the intelligence data on terrorist refuges.

Bush had directed that Pakistan receive “concurrent notification” of drone attacks, meaning they learned of a strike as it was underway or, just to be sure, a few minutes after. American drones now owned the skies above Pakistan.

In addition, McConnell had given President Bush intelligence showing that the Pakistani ISI had helped the Haqqani network attack the Indian embassy in Kabul, Afghanistan, on July 7, four months earlier. The U.S. had warned India, which had put its embassy in a defensive posture. But it was not enough. Fifty-eight people were killed and more than 100 injured in a suicide bombing.

McConnell had then moved during the September briefing to one of the most pressing worries. Al Qaeda was recruiting people from the 35 countries who didn’t need visas to enter the United States. It was paying them good money, bringing them into the ungoverned regions by the dozens, training them in all aspects of warfare—explosives and chemical—and trying to have them acquire biological weapons.

“We’re a big open sieve,” McConnell said. “They’re trying to get people with passports that don’t require a visa to get into the United States.” Al Qaeda had not succeeded yet, but that was the big worry. “We can’t find any cell in the United States, but we suspect there may be some.”

That got Obama’s full attention. Some of the 9/11 hijackers had operated for nearly 18 months in the United States before their attacks. As he had said at the end of that meeting, there were reasons to worry about winning the ele...