New York Times | By Peter Baker | 4 January 2010

The evening before he was sworn into office, Barack Obama stepped out of Blair House, the government residence where he was staying across from the White House, and climbed into an armored limousine for the ride to a bipartisan dinner. Joining him in the back seat were John Brennan, his new counterterrorism adviser, and two foreign-policy advisers, Denis McDonough and Mark Lippert. The three men with the president-elect were out of breath, having rushed more than a mile from transition headquarters on foot after failing to find a taxi in Washington’s preinaugural madness. As the motorcade moved out, they updated Obama on gathering evidence of a major terrorist plot to attack his inauguration. After a weekend of round-the-clock analysis, the nation’s intelligence agencies were concerned that the threat was real, the men told him. A group of Somali extremists was reported to be coming across the border from Canada to detonate explosives as the new president took the oath of office. With more than a million onlookers viewing the ceremony from the National Mall and hundreds of millions more watching on television around the world, what could be a more devastating target

“All the data points suggested there was a real threat evolving quickly that had an overseas component,” Juan Carlos Zarate, President George W. Bush’s deputy national security adviser for combating terrorism, told me in November. As the inauguration approached, signs of a plot “seemed to be growing in credibility and relevance.” Another senior Bush official involved in those tense events a year ago said last fall that protecting the new president was not enough. Even a failed attack would send a debilitating message to the world. “If something happens on the podium and there’s chaos,” this official told me, “that’s the first time you see the new president, and you really don’t want that.”

The threat seemed to weigh on Obama. He canceled a practice session to go over his inaugural address with aides at Blair House. David Axelrod, his senior adviser, later interpreted that as a sign that Obama was thinking about the suspected plot. “He seemed more subdued than he had been,” Axelrod told me not long ago. Obama had not yet taken office, and he was already being confronted with the threat that consumed his predecessor’s presidency. No matter how much he thought about terrorism as a senator or as a presidential candidate, it was another thing to face it as the person responsible for the nation’s security — and quite another thing again to know the threat was aimed directly at himself, his wife and their two daughters. “It’s not as if you don’t know what you’re getting into,” Axelrod said. “But when the reality comes and the baton is being passed and you’re now dealing with real terrorism threats, it’s a very sobering moment.”

There was little Obama could do but ask questions and rely on the people who had been fighting this fight for years. His advisers worked side by side with the outgoing administration. The two teams gathered in the Situation Room of the White House shortly before the inauguration to sift through what was known and to hash out what should be done about it. The final iteration of Bush’s team sat across the table from the brain trust of Obama’s administration — Condoleezza Rice, Stephen Hadley and their colleagues on one side, Hillary Rodham Clinton, James Jones and their colleagues on the other.

Clinton immediately put her finger on the problem. According to participants, she asked, what should Obama do if he is in the middle of his inaugural address and a bomb goes off somewhere on the mall? “Is the Secret Service going to whisk him off the podium so the American people see their incoming president disappear in the middle of the inaugural address?” she asked. “I don’t think so.”

Among those in the room was Robert Gates, who served two years as Bush’s defense secretary and would remain in that post under Obama. After the meeting, everyone eventually agreed that Gates should stay away from the inauguration in a secret location. With no other member of Obama’s cabinet confirmed by the Senate, Gates — an incumbent cabinet officer who also had the imprimatur of the newly elected commander in chief — was the most logical person in the line of succession to take over the presidency should the worst happen.

At the heart of the deliberations about what to do was John Brennan, a former C.I.A. officer. A Middle East specialist known for setting up the National Counterterrorism Center for Bush, Brennan was coming back after three years out of government as the top counterterrorism official in the Obama administration. He had wanted to be C.I.A. director but found his potential appointment sunk by liberal protests over his ties to the old order, so instead he was made assistant to the president for homeland security and counterterrorism and deputy national security adviser, a position that did not require Senate confirmation.