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“We’ve decimated al Qaeda’s top leadership in the border regions around Pakistan,” he told an audience on Sept. 20 at the University of Miami. “But in Yemen, in Libya, in other of these places — increasingly in places like Syria — what you see is these elements that don’t have the same capacity that a bin Laden or core al Qaeda had, but can still cause a lot of damage, and we’ve got to make sure that we remain vigilant and are focused on preventing them from doing us any harm.”

Shown those remarks recently, one intelligence source told The Times that “there’s really not a lot of daylight in that statement and where we were at the time in our assessments.”

Why it did not more regularly make its way into the president’s campaign talking points is unclear — specifically since al Qaeda in the Arabian Peninsula had factored into multiple U.S.-focused terrorist plots foiled during Mr. Obama’s first term.

In his statement to The Times, Mr. Ruppersberger described al Qaeda in the Arabian Peninsula as “the ‘affiliate’ that is the strongest and the consensus assessment is that it is a threat to U.S. interests.”

“We now know that there is contact between AQAP and core AQ,” he said.

The intelligence community’s focus on AQAP shifted as far back as 2009, when the group claimed responsibility for the failed Christmas Day plot in which a 23-year-old Nigerian attempted to ignite a clutch of plastic explosives sewn to his underwear aboard a Northwest Airlines flight from Amsterdam to Detroit.

AQAP’s support for such a plot — with no obvious strategic connection to the group’s localized focus in Yemen — suggested the hidden hand of al Qaeda’s leadership was at play.

Debate on the question was still swirling through Congress after the 2012 election when Republicans on the Senate Select Committee on Intelligence pressed John O. Brennan, in his confirmation hearing to be CIA director, to opine publicly on the influence exerted over the affiliates by al Qaeda’s core leadership.

“We do see al Qaeda core trying to exert some control over some of these elements,” Mr. Brennan said in response to a question from Sen. Daniel Coats, Indiana Republican.

Sen. Susan M. Collins, a Maine Republican who was new to the committee, suggested that al Qaeda was not so decimated as Mr. Obama sought to portray it on the campaign trail.

“If you look at a map today, you would see al Qaeda in all sorts of countries,” said Mrs. Collins. “That’s not to say that there weren’t cells in other countries back in 2001, but it raises the question in my mind of whether, even though we’ve been successful in taking out some of the core of al Qaeda and some high-level leaders, whether our strategy is working.”

Mr. Brennan acknowledged that “al Qaeda and this — you know, the forces of Islamic extremists, that have really corrupted and perverted Islam, are making some progress in areas that give me real concern.”

Mrs. Collins told The Times that despite successes against the “core” in Pakistan and Afghanistan, “the fact is that the Islamist extremist threat has metastasized to other countries.”

AQAP in Yemen, Mrs. Collins said, “has become the new ‘core’ al Qaeda in many ways, posing a threat to the region and to Western targets, including the United States.”

“We must be clear-eyed,” she said, “in recognizing that ‘core’ al Qaeda in Afghanistan and Pakistan is not the only location from which attacks can be planned.”

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