The crucial intercept that prompted the U.S. government to close embassies in 22 countries was a conference call between al Qaeda’s senior leaders and representatives of several of the group’s affiliates throughout the region.

The intercept provided the U.S. intelligence community with a rare glimpse into how al Qaeda’s leader, Ayman al-Zawahiri, manages a global organization that includes affiliates in Africa, the Middle East, and southwest and southeast Asia.

Several news outlets reported Monday on an intercepted communication last week between Zawahiri and Nasser al-Wuhayshi, the leader of al Qaeda’s affiliate based in Yemen. But The Daily Beast has learned that the discussion between the two al Qaeda leaders happened in a conference call that included the leaders or representatives of the top leadership of al Qaeda and its affiliates calling in from different locations, according to three U.S. officials familiar with the intelligence. All told, said one U.S. intelligence official, more than 20 al Qaeda operatives were on the call.

To be sure, the CIA had been tracking the threat posed by Wuhayshi for months. An earlier communication between Zawahiri and Wuhayshi delivered through a courier was picked up last month, according to three U.S. intelligence officials. But the conference call provided a new sense of urgency for the U.S. government, the sources said.

Al Qaeda members included representatives or leaders from Nigeria’s Boko Haram, the Pakistani Taliban, al Qaeda in Iraq, al Qaeda in the Islamic Maghreb, and more obscure al Qaeda affiliates such as the Uzbekistan branch. Also on the call were representatives of aspiring al Qaeda affiliates such as al Qaeda in the Sinai Peninsula, according to a U.S. intelligence official. The presence of aspiring al Qaeda affiliates operating in the Sinai was one reason the State Department closed the U.S. Embassy in Tel Aviv, according to one U.S. intelligence official. “These guys already proved they could hit Eilat. It’s not out of the range of possibilities that they could hit us in Tel Aviv,” the official said.

Al Qaeda leaders had assumed the conference calls, which give Zawahiri the ability to manage his organization from a remote location, were secure. But leaks about the original intercepts have likely exposed the operation that allowed the U.S. intelligence community to listen in on the al Qaeda board meetings.

“This was like a meeting of the Legion of Doom,” one U.S. intelligence officer told The Daily Beast, referring to the coalition of villains featured in the Saturday morning cartoon Super Friends. The official said Zawahiri announced to the broader organization during the meeting that Wuhayshi had been promoted to “Ma’sul al-Amm,” an Arabic term that roughly translates as “general manager.” The promotion effectively gave the leader of al Qaeda’s affiliate in Yemen operational control of al Qaeda’s many affiliates throughout the Muslim world, the official said, a key factor that led the State Department to close embassies, missions, and consulates throughout the region. “All you need to do is look at that list of places we shut down to get a sense of who was on the phone call,” the official said.

Also during the meeting, the various al Qaeda leaders discussed in vague terms plans for a pending attack and mentioned that a team or teams were already in place for such an attack. For some leading members of Congress, the revelation that al Qaeda’s leadership in Pakistan is actively managing and directing the operations of several affiliates directly refutes the Obama administration’s repeated assertion that the leadership of the core of the group has been decimated by American drone strikes and special operations forces while the affiliate groups have been strengthened.

“This may punch a sizable hole in the theory that al Qaeda is on the run,” Sen. John McCain (R-AZ) told The Daily Beast on Tuesday.

During the 2012 presidential campaign, Obama often said that his administration’s actions put al Qaeda “on its heels,” although he later amended that claim to specify that he was referring to al Qaeda’s core leadership in Afghanistan and Pakistan. The administration continued to make that argument Monday.

“We’ve been clear that we have made a great deal of success against al Qaeda core in Afghanistan and Pakistan, that we have taken a number of steps to really decimate that group’s leadership, including, of course, most importantly, Osama bin Laden,” said State Department deputy spokeswoman Marie Harf on Monday. “But at the same time, we’ve all made clear, from the president on down, that we remain very concerned about the affiliates, al Qaeda affiliates throughout the world. And in that—first on that list is always AQAP.”

McCain said not only are the affiliates gaining strength but also that the core al Qaeda leadership in Pakistan is showing resilience, as evidenced by this latest news.

“The core seems to be able to able to reconstitute itself. The core also seems to be able to coordinate and manage the affiliates,” he said. “There was a gross underestimation by this administration of al Qaeda’s overall ability to replenish itself.”