Notwithstanding Janet Napolitano’s statement last month that “the system worked,” Obama suspected that it had not. While on vacation he was given an 80-page review of the Fort Hood shooting, looking at how information about Hasan was not well circulated within the federal government. The night after his first statement, his advisers learned that something similar happened in this case: the government possessed National Security Agency-intercepted conversations that could have helped to stop Abdulmutallab if they had been shared widely.

Obama talked with Brennan and other advisers by phone the next morning. He was simmering. “Let me make this very clear to you,” he told the advisers, according to two of them. “While I understand intelligence is hard, and I’ll never fault anybody for not having full intelligence, what I will fault is when we have full intelligence that’s not shared.” After hanging up with Brennan, aides scrambled to organize a statement to the news media. Denis McDonough, the National Security Council chief of staff, typed out a draft on the president’s laptop as Obama hovered over his shoulder.

“What’s the deal?” Obama asked.

“I’m just about done,” McDonough said.

“Well, just move over.” Obama sat down and finished it himself.

The president’s statement that there was a “systemic failure” did not quell the political furor, and White House officials were caught off guard by the intensity of the criticism. After reading a Cheney statement that attacked Obama for only pretending to be at war with terrorists, David Axelrod angrily wrote a long statement trashing the former vice president and gave it to Dan Pfeiffer, the White House communications director, who revised it and posted on the White House Web site. The criticism got Brennan’s back up too, particularly coming from some of his former colleagues in the Bush administration.

“A lot of the knuckleheads I’ve been listening to out there on the network shows don’t know what they’re talking about,” he told me after the Christmas Day attempt. Some Republicans, including Cheney, were blatantly mischaracterizing the record, he fumed. “When they say the administration’s not at war with Al Qaeda, that is just complete hogwash.” It was the angriest I had heard him during months of conversations. “What they’re doing is just playing into Al Qaeda’s strategic effort, which is to get us to battle among ourselves instead of focusing on them,” he said.

It is moments like these when Brennan’s disaffection from the last administration becomes evident. “I much prefer talking with someone who is interested in understanding the situation and responding to it appropriately,” Brennan told me.

For all of the attention on the Nigerian underwear bomber, some experts say they believe the more insidious threat will be a new generation of homegrown extremists. In recent months, authorities have arrested a number of American residents, including Najibullah Zazi, an airport-shuttle driver who is suspected of plotting to attack New York after receiving training in Pakistan, and David Coleman Headley, a Pakistani-American accused of aiding terrorist attacks in Mumbai. There was the Fort Hood shooting rampage, as well as a group of Somali-Americans from Minnesota who reportedly wanted to fight in Somalia and five American Muslims from Virginia who traveled to Pakistan supposedly to join the jihad.

If they are the next wave, American extremists are going to be hard to track and stop. The Internet makes it possible for Al Qaeda and its allies to reach out from the dusty villages of Waziristan all the way to Illinois and Colorado. “Although no one wants to admit it, I think a watershed has been crossed in the terrorist threat in the United States,” Bruce Hoffman, a Georgetown University terrorism scholar, told me. “It’s way different than it was in the Bush years.”

The Obama administration has been trying to figure out how to counter it. In October, Obama secretly ordered a review of the ways different agencies track travels between the United States and places like Pakistan to look for holes to close. Napolitano told me: “We can’t operate in the paradigm that if they attack us, they would be coming from other countries into the United States. We have some that are homegrown. That is a change.”

After all the lawyerly focus on Guantánamo and the rules of war, the latest threats put more focus on Obama in the role of commander in chief. It did not go unnoticed that when he accepted the Nobel Peace Prize last month, he declared that “evil does exist in the world.” His press secretary, Robert Gibbs, went on the Sunday shows after the Christmas Day plot and, consciously or not, used the term “war on terror.”

The White House then dispatched Brennan for a blitz of four Sunday shows, the first such foray for the C.I.A. veteran. In his first radio and Internet address of the new year, Obama implicitly rebutted Cheney by noting that he used the word “war” is his inaugural address. “Our nation is at war against a far-reaching network of violence and hatred,” Obama said.

The war goes on, abroad and at home.

An earlier version of this article referred imprecisely to John Brennan. While he is a deputy national security adviser, his official title is assistant to the president for homeland security and counterterrorism.

Source: NYT