It’s hard to imagine an American leader authorizing the shoot-down of civilian aircraft. But in the first hour following the attacks of September 11, 2001, when it was unclear how many passenger jets had been weaponized by terrorists—and then aimed at America’s seats of power—that’s exactly what happened.

According to what historic record exists from that chaotic morning, however, it’s unclear that the decision came directly from someone in the operational chain of command, which runs from the President to the Secretary of Defense down to military commanders. President George W. Bush, who began the day at an education event in Florida, was sequestered in the skies on Air Force One, frustrated by scant information, spotty communication and handlers determined to keep him safely away from the capital. Secretary of Defense Donald Rumsfeld, meanwhile, became unreachable after the Pentagon itself had been struck.

That left Vice President Cheney, positioned in a bunker beneath the White House, in the decision-making hot seat.

Moments after the second plane crashed into the World Trade Center’s South Tower at 9:03 a.m., it became clear America was under attack. With word that radar had spotted a plane heading straight for the White House, the executive mansion was evacuated and Secret Service agents quickly hustled Cheney and a handful of other high-ranking administration officials down the basement corridors to a Cold War-era underground bunker. During the first hour there, confusion reigned as the team watched the news unfold on TV and struggled to gather reliable information about the unprecedented attack from the Federal Aviation Administration, the Federal Emergency Management Agency, the Central Intelligence Agency and the Pentagon. The most immediate questions revolved around how many planes remained in the sky, how many had been commandeered by hostile forces—and what to do about it.

As part of the research for my book, The Only Plane in the Sky: An Oral History of 9/11, I interviewed dozens of top U.S. officials who were with the president and vice president that day—as well as culled official oral histories conducted by the Pentagon and other institutions in the wake of 9/11—to create one of the most detailed pictures yet of the national decision-making that unfolded that morning.

One particular moment of that first hour in the bunker would prove among the day’s most controversial moments: that order from Cheney authorizing fighter jets to shoot down hijacked airliners. Did he actually have the authority to give the order? And did he and President Bush connect before or after Cheney ordered the fighters into battle?

The White House bunker, known officially as the Presidential Emergency Operations Center (PEOC), dates back to World War II, when officials set up a modest bunker for Franklin D. Roosevelt in the event of a surprise German attack on the capital. Harry Truman expanded the facility dramatically for the Cold War as part of a large White House renovation during his presidency. In the years since, the bunker has been updated technologically; and while officials and presidents had used it as part of drills and exercises, it had never been used for its intended purpose—until 9/11.

Still, the facility is staffed 24 hours a day, and that morning the team on duty had been gathering for its normal Tuesday morning staff meeting when the towers were struck. Within minutes, Vice President Cheney and other officials arrived. Navy Commander Anthony Barnes was on duty that morning, and in his first-ever interview, he recalls that he looked around and saw National Security Advisor Condoleezza Rice, White House Communications Director Karen Hughes, Cheney aide Mary Matalin and Secretary of Transportation Norman Mineta: “Mr. Mineta put up on one of the TV monitors a feed of where every airplane across the entire nation was. We looked at that thing—there must have been thousands of little airplane symbols on it.”

Barnes, who served on 9/11 in a role known as the deputy director of Presidential Contingency Programs—that is, the deputy director of the nation’s doomsday plans at the White House—explains, “The PEOC is not a single chamber; there are three or four rooms. The operations chamber is where my watch team was fielding phone calls. Then there’s the conference room area where Mr. Cheney and Condi Rice were—that’s the space that had the TV monitors, telephones, and whatever else.”

In those opening minutes of the crisis response, officials still struggled to understand what was happening—particularly as word came around 9:37 a.m. that the western face of the Pentagon had been hit too, targeted by American Airlines Flight 77, hijacked out of Dulles International Airport.

**"**That first hour was mass confusion because there was so much erroneous information," recalls Barnes. "It was hard to tell what was fact and what wasn’t. We couldn’t confirm much of this stuff, so we had to take it on face value until proven otherwise."

Remarkably, one of the reasons Cheney was left seemingly on his own during that first hour of the crisis was because Defense Secretary Donald Rumsfeld, officially the second person in the military chain of command, rushed out of his Pentagon suite in the moments after the attack and went to the crash site personally.

Under the protocols for the secret system known as “continuity of government,” meant to preserve the U.S. leadership and evacuate key officials to bunkers and mobile command posts around Washington in the event of an attack, Rumsfeld should have been immediately evacuated. Yet that day he found himself torn between his official duties and the unfolding human tragedy. His actions that morning, where he actually helped carry stretchers of wounded personnel out of the impact zone, would long endear him to the military. But placing himself in danger—and out of communication in a moment of true crisis—was precisely the wrong action from an official standpoint.

As Victoria “Torie” Clarke, the head of public affairs at the Pentagon, recalled in her oral history, not even Rumsfeld’s staff fully understood where he was in the moments after the attack: “Several times in the next half-hour or so people would ask where the secretary was. The answer was ‘out of the building.’ We took that to mean that he had been taken to a secure location. But he had gone out to the [crash] site.”

Aubrey Davis, one of Rumsfeld’s security agents who trailed the defense secretary out to the crash, recalls hearing frantic questions on the radio about the secretary’s whereabouts that he was unable to answer: “The Communications Center kept asking where the secretary was, and I kept saying we had him. They couldn’t hear.”

At the White House, aides feared the worst for Rumsfeld. As Mary Matalin recalls, “There was a real concern in getting information about the casualties at the Defense Department. At first, we thought Secretary Rumsfeld had been hit, then we heard he was pulling bodies out of the rubble. We couldn’t quite get a location on the Secretary of Defense.”

That vacuum—with the “SecDef” beyond reach and the president himself being hustled aboard Air Force One in Florida—meant that Cheney faced the critical hour from 9:30 a.m. to 10:30 a.m. almost entirely alone. They struggled to piece together what was happening. As Barnes says, “Every one of my guys in the watch room have at least two phones to their ears. I was talking to the Pentagon operations center on one line. I had a line to FEMA, and people are asking us for directions on what to do and how to do it.”

Matthew Waxman, an aide on the National Security Council, recalls how difficult it was to get information at the time. “The TV feeds would occasionally go down. The vice president was pretty ticked off about that. There were technical glitches that day,” he told me. “One of my jobs was to stand with a phone in my hand to make sure that there was an open line between the PEOC and some of the other national security officials. So that if the vice president or the National Security Adviser needed to speak to one of them, we had a direct line out with me at one end and a counterpart on the other.”

One of the most critical questions to arise was how to handle the remaining hijacked planes—no one from air traffic control or the military was really sure how many planes in the air were still under the control of terrorists, but they feared the number might be a dozen or more.

Then, at 9:59 a.m., the morning went from very bad to worse as the South Tower collapsed in a rolling cloud of dust. As Barnes says, “There are four or five very large, 55-inch television screens in the PEOC...I remember Cheney being as flabbergasted as the rest of us were sitting there watching on these monitors. Back in those days, a 55-inch TV monitor was a really big TV. It was almost bigger than life as the towers collapsed.”

A moment of truth arrived sometime shortly thereafter, around 10 a.m., likely between 10:12 a.m. and 10:18 a.m., according to the best reconstruction later. As Barnes, who has never before spoken publicly about the morning, explains, “The Pentagon thought there was another hijacked airplane, and they were asking for permission to shoot down an identified hijacked commercial aircraft. I asked the Vice President that question and he answered it in the affirmative. I asked again to be sure. ‘Sir, I am confirming that you have given permission?’ For me, being a military member and an aviator—understanding the absolute depth of what that question was and what that answer was—I wanted to make sure that there was no mistake whatsoever about what was being asked. Without hesitation, in the affirmative, he said any confirmed hijacked airplane may be engaged and shot down.”

Cheney didn’t blink at the order. Scooter Libby, his chief of staff, recalled that the vice president decided “in about the time it takes a batter to decide to swing.” As Cheney himself explained later, “It had to be done. Once the plane became hijacked—even if it had a load of passengers on board who, obviously, weren’t part of any hijacking attempt—having seen what had happened in New York and the Pentagon, you really didn’t have any choice. It wasn’t a close call.”

A question, though, has lingered ever since: The vice president isn’t actually part of the military chain of command and, in theory, doesn’t have authority to order fighters into battle—let alone to take an unprecedented step of shooting down a commercial domestic airliner filled with civilians. According to standard protocols, such an order should only come from the president.

It’s not clear—and years of extensive investigation has never definitively determined—whether Cheney had actually spoken to President Bush to get such an authority. Both men have hinted that they’d spoken prior to Cheney’s order, but there’s little concrete evidence they did. In fact, the preponderance of evidence appears to show that Vice President Cheney unilaterally gave the order.

According to the 9/11 Commission, White House Deputy Chief of Staff Joshua Bolten—the senior-most of the president’s staff at the White House that day—was present when Cheney gave the authorization to Barnes. The 9/11 Commission reported that “Bolten watched the exchanges and, after what he called ‘a quiet moment,’ suggested that the vice president get in touch with the president and confirm the engage order. Bolten told us he wanted to make sure the president was told that the vice president had executed the order. He said he had not heard any prior discussion on the subject with the president.”

Cheney has long insisted that he had spoken to the president before giving the order to Barnes, but there’s no proof of such a call. Some of the best possible evidence comes from the recollection of Condoleezza Rice, who told the 9/11 Commission that when she entered the PEOC, she heard the vice president on the phone with the president. She said she “remembered hearing him inform the president, ‘Sir, the [Combat Air Patrols] are up. Sir, they're going to want to know what to do?’ Then she recalled hearing him say, ‘Yes sir.’”

That conversation, though, seems unlikely to have been placed accurately in the morning’s timeline—the Combat Air Patrols launched by the Air Force and various Air National Guard units that morning were largely not in place until the early part of the 10 a.m. hour, although there were fighter jets from Otis Air Force Base on Cape Cod over New York City by a little after 9 a.m.

What is clear is that President Bush concurred with the order, whenever he and Cheney did speak. The two men spoke at 10:18 a.m., with the president safely aboard Air Force One, and contemporaneous notes from the plane by White House Press Secretary Ari Fleischer note at 10:20 a.m., President Bush told aides that he had authorized hijacked planes to be shot down. As White House Chief of Staff Andy Card told me, “The president is sitting at his desk, and I’m sitting directly in front of him. I witness the president authorize the Air National Guard to shoot down the hijacked airliners. The conversation was sobering to hear. What struck me was as soon as he hung up the phone, he said, ‘I was an Air National Guard pilot—I’d be one of the people getting this order. I can’t imagine getting this order.’”

While Barnes says that in the PEOC he never wondered whether Flight 93 had been shot down by U.S. fighters—he says he heard none of the “chatter” from the military side that would have indicated a fighter had unleashed a weapon in American airspace—those on Air Force One were less sure. For much of the morning, those with the president thought it possible their decisions had resulted in the plane’s downing. As Andy Card told me, “We hear that Flight 93’s gone down. We’re all wondering, _Did we do that?..._It lingered deepest in the president’s conscience.”

Around 10:30 a.m., Rumsfeld himself was back in command at the Pentagon’s nerve center, the National Military Command Center, and spoke to the vice president by phone at 10:39 a.m. “There’s been at least three instances here where we’ve had reports of aircraft approaching Washington,” Cheney told the defense secretary. “Pursuant to the president’s instructions I gave authorization for them to be taken out.”

Rumsfeld gave no immediate response. Cheney heard only silence and asked, “Hello?”

Finally Rumsfeld replied, “Yes, I understand. So we’ve got a couple aircraft up there that have those instructions at this present time?”

“That is correct,” Cheney said, “and it’s my understanding they’ve already taken a couple aircraft out.”

As John Farmer, Jr., senior counsel of the 9/11 Commission, later recounted, the conversation between Cheney and Rumsfeld was “remarkable, ultimately not as an artifact of history but as an indication of how little-understood the events of the morning remained years later, even—and perhaps especially—to national leaders.” As he said, “They honestly believed that their actions in those critical moments made a difference; the records of the day say otherwise.”

Indeed, the question of whether Cheney technically had the authority to give that shoot-down order ends up being somewhat academic. Had it even been conveyed to fighters in the air fast enough, it would have meant little: United Airlines Flight 93, the final hijacked plane, crashed in a Pennsylvania field at 10:03 a.m., minutes before Cheney’s exchange in the PEOC. In fact, according to the 9/11 Commission and its reconstruction of the morning’s events, it wasn’t until 10:31 a.m. that Cheney’s order even reached the military. Had Flight 93 continued on its path, the hijacked plane would have reached the nation’s capital sometime between 10:13 and 10:23 a.m.

While most speculate that Flight 93 was targeting the Capitol—the White House is a much smaller, harder to hit target—to this day no one knows for sure.

Garrett M. Graff, a journalist and historian, is the author of The Only Plane in the Sky: An Oral History of 9/11 (Avid Reader Press). He can be reached at garrett.graff@gmail.com.

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