A secret message that was intercepted between al-Qaeda chief Ayman al-Zawahri and his deputy in Yemen led to the shutdown of US embassies.

A US intelligence official and a Mideast diplomat say al-Zawahri’s message was picked up several weeks ago and appeared to initially target Yemeni interests.

A senior official with Iraq’s interior ministry told CNN on condition of not being identified that top officials of al Qaeda in Iraq, including Adnan Ismail Najim Abdullah al-Dulaimi, escaped from Abu Graib prison during the jailbreak there last month and remains at large.

Bergen noted that a 2006 prison break in the Yemeni capital, Sanaa, led to the creation of al Qaeda in the Arabian Peninsula, one of the terrorist organization’s most virulent affiliates.

Although the prison breaks are not the main reason for the raised terror threat, said CNN Terrorism Analyst Paul Cruickshank, “it is part of the background music.” Prison breaks can often strengthen terrorist groups because “some of these guys are likely to be seasoned operatives,” he added.

[Jay] Carney said that the “president has been clear that the threat from Al Qaeda very much remains,” and said officials were particularly concerned about affiliates of the terror group outside its main “core” in Afghanistan and Pakistan.

“As Al Qaeda’s core has been diminished through the efforts of the United States and our allies, affiliate organizations, including in particular, Al Qaeda in the Arabian Peninsula, have strengthened. We have here in Washington have identified AQAP in particular as the dangerous threat,” Carney said.

Carney added that the affiliate groups had been a point of focus “for some time now,” and said the U.S. had “focused a great deal of attention on those affiliated organizations.”

Widespread U.S. embassy closures and travel alerts prompted by al Qaeda’s affiliate in Yemen show how the group has proved stubbornly resilient despite more than two years of American strikes against its leaders…

The high level of concern from U.S. officials underscores what many in the intelligence world have long warned. While al Qaeda’s central leadership may be weakened, the rest of the group has morphed into smaller entities and dispersed, which has made the threat harder to predict and track. This process was accelerated by the turmoil of the Arab Spring…

Beyond Yemen, al Qaeda in Iraq has reconstituted itself. Its branch in Syria is drawing in hundreds of foreign recruits each month. And in Mali, al Qaeda-linked fighters fled French warplanes and commandos and have set up a rudimentary base in the Libyan Desert outside Paris’s reach…

The death of several high-ranking members of the group and the absence of any serious threats for more than a year “may have lulled us into thinking the threat from that group had passed,” he said.

The fact that Asiri and his associates, both in Yemen and elsewhere in the Arab world, retain the ability to cause a global security alert suggests that, for all the efforts undertaken by Western counter-terrorism agencies, al-Qaeda remains a considerable threat to our security.

The widespread closure of diplomatic missions over the weekend certainly appears to contradict President Obama’s claim last summer that the “war on terror” was drawing to a close, and that the al-Qaeda organisation originally founded by Osama bin Laden no longer had the ability or capacity to cause wholesale carnage in the West…

Certainly, to judge by the recent upsurge in al-Qaeda activity, the organisation is currently experiencing something of a renaissance…

American special forces units overseas have been on alert for the past several days for a mission to attack potential al Qaeda targets if those behind the most recent terror threats against U.S. interests can be identified, a senior Obama administration official told CNN.

The official declined to identify the units or their locations because of the sensitive nature of the information.

There are two pieces of news there. The reason for the shuttering the embassies is interesting, of course. But the far more significant development is the disclosure of the fact that the U.S. government intercepted communications that included some of those to or from Zawahiri. It seems clear that however Zawahiri and Wuhayshi were communicating, they won’t likely be in touch the same way again. As a result, the United States stands to lose access to realtime intelligence from one or both of these top al Qaeda leaders.

In a story published Sunday, McClatchy reported on the source of the intelligence. “An official who had been briefed on the matter in Sanaa, the Yemeni capital, said the embassy closings and travel advisory were the result of an intercepted communication between Nasir al-Wuhayshi, the head of the Yemen-based al-Qaida in the Arabian Peninsula, and al-Qaida leader Ayman al Zawahiri in which Zawahiri gave ‘clear orders’ to al-Wuhaysi, who was recently named al Qaida’s general manager, to carry out an attack. The official, however, said he could not divulge details of the plot.”…

Whatever comes of these warnings, and we downplay them are our peril, the disclosure of the fact that the U.S. government issued them because of intercepted communications between al Qaeda leaders necessarily makes us less secure.

Finally, Mr. Obama believed that defeating “core al Qaeda”—the group around Osama bin Laden in Pakistan and Afghanistan—effectively meant defeating al Qaeda, even if a few of its lesser offshoots in Africa or the Arabian Peninsula survived. In fact, al Qaeda was designed not as an organization with subordinate branches, but as a model with multiple franchises—as Burger King not General Motors.

In his speech, Mr. Obama insisted that “not every collection of thugs that labels themselves al Qaeda will pose a credible threat to the United States.” Yet if al Qaeda in Mesopotamia, or the Arabian Peninsula, or the Maghreb, or some as-yet unknown al Qaeda affiliate succeeds in bombing a U.S. embassy, taking down an airliner, or engineering a second 9/11, will it matter that the plot was hatched in Yemen or Somalia instead of Pakistan or Afghanistan?

Which brings us to the shortest distance in Washington: the one that runs between an Obama speech and the media’s memory of it. The speech at the National Defense University was billed as a major presidential address. A lengthy article in the New York Times, written days later, reported it was a “window into the presidential mind,” the result of “an exercise lasting months,” a matter not just of Mr. Obama’s policy, but of his very legacy.

Yet here we are, not three months later, faced with a threat that makes a comprehensive and vivid mockery of everything the president said.