When chief of staff Andrew Card knelt down and told George Bush “America is under attack” 15 years ago Sunday, the words he whispered in the president’s ear in a Florida classroom launched what was supposed to be a planned, orderly response to a national emergency.

But what followed instead was chaos, a breakdown in communication and protocol that risked international conflict and could have made Sept. 11, 2001, a still bigger tragedy. There were live nukes on the tarmac at U.S. airbases, a failed communications system, and a security protocol for the president and his potential successors — the “continuity of government” plan — that only one top official followed.

Based on a review of newly unclassified documents, memoirs and other published accounts, and interviews with U.S. officials, NBC News has learned that:

Three dozen live nuclear weapons were aboard U.S. Air Force bombers at three airbases when al Qaeda struck New York and Washington.

Because of inadequate communications equipment and procedures, top U.S. officials couldn’t talk to each other or to anyone else. Russian President Vladimir Putin wanted to speak to Bush to know why the U.S. was preparing to go to DEFCON 3 — but the White House couldn’t put him through to Air Force One. Bush had no way to receive phone calls.

After Bush left Florida, where he had been reading a book to schoolkids, his plane was low on fuel but for hours had nowhere to land.

Most of the top 10 people in the president’s line of succession, including Vice President Cheney and Donald Rumsfeld, either refused to follow the protocol and go to their designated secure sites, or were out of the country, or were never contacted.

Now-disgraced Speaker of the House Denny Hastert, third in line, observed protocol and was taken to an underground bunker in the Blue Ridge Mountains. But that left him out of touch with all other top government leaders.

Attorney General John Ashcroft was in a government plane and tried to return to Washington, but was turned away by the FAA.

Education Secretary Rod Paige, 16th in line to the White House, was left on the tarmac in Sarasota, Florida. He rented a car and drove back to Washington.

Because of the confused response on 9/11, the U.S. made several changes to its continuity of government protocol and its security preparations in the event of another attack on the capital.

There is a new hardened bunker for top White House officials in the Washington, D.C. suburbs.

A number of mobile missile batteries are deployed around the Washington area. Their locations are not disclosed and they are moved regularly.

A new, secure communications system has been built in Wyoming that can keep top officials connected 24/7 should an emergency arise.

On Sept. 11, 2001, hijackers attacked New York City's World Trade Center. Sean Adair / REUTERS

But past experience suggests that the “continuity of government” protocol may still be difficult to execute in the event of another crisis. After all, the plan had to be revised after glitches in the response to the attempted assassination of Ronald Reagan in 1981 and again after a 1983 war game that the Russians mistook for the real thing, only to be swamped by the confusion of Sept. 11.

War Games Turn Real World

Perhaps the biggest newly uncovered secret is that on the morning of 9/11, when Al Qaeda struck New York and Washington, the Pentagon’s annual “Global Guardian” war game was in full swing. Three dozen real nuclear weapons had been loaded onboard intercontinental bombers in North Dakota, Missouri, and Louisiana.

When Bush left Florida on Air Force One amid fears that terrorists would try take down the presidential plane, he flew right into the middle of the war game.

Air Force One had climbed out of Sarasota airport 51 minutes after American Airlines Flight 11 plowed into the North tower of the World Trade Center and 12 minutes after the Pentagon was struck. The fourth and final hijacked passenger plane, United Flight 93, was still aloft over Pennsylvania.

According to a new Pentagon history of 9/11, the pilot of Air Force One “flew the plane as high and fast as possible for better security.” The president’s aircraft can — and did — fly as high as 48,000 feet that day.

Because of intelligence of a specific terrorist threat to “Angel,” the codename for the President’s plane, Bush was sent essentially into orbit. His plane was low on fuel, and had no firm destination. The Bush national security team finally selected Barksdale Air Force Base outside Bossier City, Louisiana, as a place to put down temporarily because it had a secure area for refueling.

Adm. Richard Mies, the commander of U.S. Strategic Command (STRATCOM), which was overseeing the war game, had pulled the plug on the exercise as soon as he heard the news of the attacks in Washington and New York, according to an interview published this week in the Omaha World-Herald.

The game had turned “real world,” as the military likes to say, with war planners considering the various scenarios — the scariest of which was a terrorist plane attacking one of the airbases hosting nuclear warheads. Barksdale, where Bush was headed, was one of the primary B-52 bomber bases in the world.

President Bush is interrupted at 9:07 a.m. during a school visit in Sarasota, Florida., by Andrew Card, his chief of staff, and informed that a second plane has hit the World Trade Center. PAUL J. RICHARDS / AFP

“You would destroy half of Bossier City with the explosions,” Al Buckles, Strategic Command’s watch officer that day, revealed to the Omaha World Herald last week. “Nuclear weapons were exposed.”

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When STRATCOM got word that President Bush wanted to land at Barksdale, munitions specialists scrambled to finish unloading the bombers.

Meanwhile, the Russians were calling. They had detected preparations for a readiness increase of U.S. military forces — DEFCON 3 — scheduled for implementation at 10:53 EST.

Gen. Ralph “Ed” Eberhart, the commander of North American Aerospace Defense Command in Colorado Springs that day, told the 9/11 Commission in now-declassified Top Secret testimony that moving to DEFCON 3 was hotly debated. It was not intended for 9/11 type scenarios, but rather nuclear war. It “could have complicated the response to the attacks,” Eberhart noted.

“We had the president, who didn’t want to follow our plans for a nuclear attack"

Rather than stand-down nuclear forces, as STRATCOM was doing at Barksdale, DEFCON response rules directed increased readiness. And if the alert level moved to DEFCON 2, the next highest level, nuclear weapons would again have to be reloaded on the B-52’s.

With U.S. forces worldwide going on alert, the U.S. ambassador to Moscow, Alexander Vershbow, called the White House Situation Room: Russian President Vladimir Putin “wanted to speak with Bush.”

Coincidently, the Russians were in the middle of their own nuclear war exercise and their intelligence had now detected telltale signs of enhanced American force posture.

For 30 minutes, White House communicators tried to establish a secure line between Air Force One and the Kremlin, finally giving up. Russian-speaking National Security Advisor Condoleezza Rice then got on the phone with the Russian president to agree on a cooperative stand-down.

Rice was in the underground bunker beneath the East Wing of the White House with Vice President Cheney and Secretary of Transportation Norman Mineta, who was directing the FAA’s decision to clear American skies of all aircraft.

Still in limbo, Air Force One was circling over Northern Florida.

And inside the plane, Bush was furious, virtually unable to communicate with the outside world at a time of crisis.

Those on board were told to switch their cell phones off so the plane could not be tracked. Bush could talk to Dick Cheney, but the official communicators hadn’t been able to put a call through to his wife Laura for more than three hours. “I couldn’t believe that the president of the United States couldn’t reach his wife in the Capitol Building,” Bush later wrote in Decision Points.

To add fuel to Bush’s fire, the Secret Service and his national security team also discouraged him from returning to Washington, worrying that the capital was still a target.

“We had the president who didn’t want to follow our plans for a nuclear attack, which is hide him, keep him safe and allow continuity of government,” says Air Force One pilot Mark Tillman, a now retired Air Force Colonel who wrote his own book about that day.

After 40 minutes of circling over Florida, the decision was finally made to land at Barksdale, where the plane could refuel, and the President could record a short statement from the Commander-in-Chief.

Air Force One touched down at 11:40 AM, while the nuclear weapons were still being unloaded just a few hundred feet away, according to a STRATCOM deputy, who spoke to NBC News after Mies revealed the still secret nuclear weapons connection in the Omaha World-Herald.

Left behind in Sarasota, though, was Secretary of Education Rod Paige. He’d gone to Emma Booker Elementary School with the President that morning, but was left at the school when Air Force One took off. Paige, 16th in line to succeed the president, made his own way back to Washington in a rental car.

Cheney and Rumsfeld Say No

Bush ultimately flew back to Washington, after stopping at STRATCOM headquarters at Offutt Air Force Base in Nebraska. By then it was clear he wasn’t the only member of the line of succession who wasn’t following the continuity of government plan.

Had Air Force One been attacked, and had the White House been hit by United Airlines Flight 93 as the terrorists intended, the list of who would be in charge turns into a tangled mess.

The first in line to succession, Cheney, stayed at the White House. Cheney wrote in his autobiography, "In My Time: A Personal and Political Memoir," that when his aide told him that he had to evacuate to his designated bunker outside Washington, he looked at him like he was insane and said he wasn’t going anywhere.

If Cheney had been killed, presidential succession would have passed to Speaker of the House Dennis Hastert, who was third in line. Unlike other top officials, he followed protocol on 9/11. He was whisked away to Mount Weather, an underground bunker in the Blue Ridge Mountains of western Virginia. There, he spent the day out of touch with the national leadership.

The fourth in line, 83-year old Sen.Robert Byrd of West Virginia, also refused to go anywhere and was taken to his Capitol Hill home.

The fifth in line to be president, Secretary of State Colin Powell, was in Peru.

The sixth, Treasury Secretary Paul O’Neill, was in Japan.

Smoke comes out from the Southwest E-ring of the Pentagon building September 11, 2001 in Arlington, Virginia after a plane crashed into the building and set off a huge explosion. Alex Wong / Getty Images

The seventh, Defense Secretary Donald Rumsfeld, was in a smoldering Pentagon, and also refused to evacuate. He instead sent his deputy Paul Wolfowitz to “Site R,” the underground bunker at Raven Rock on the Maryland-Pennsylvania border.

Eighth in line, Attorney General John Ashcroft, was in a government plane. When he ordered it turned around to return to the capital, the FAA wouldn’t let him enter Washington airspace.

The ninth in line, Agriculture Secretary Ann M. Veneman, was never contacted, according to White House records.

Commerce Secretary Don Evans, 10th in line, waited in his downtown office for someone to contact him to tell him what to do; and when no one did, he had an aide drive him home to McLean, where he sat and watched television.

Layer upon layer of systems and contingency plans, some 50 years old, had been created and tweaked more than once. But on that day, not one of the principals knew the plans in any detail and four of the five top successors to the presidency declined to follow the continuity of government protocols.

The system that has been set up is so secret, even the 9/11 Commission was unable to penetrate what really happened that day. It was stonewalled by guardians of the “special program” and thwarted by a nervous White House that was uniquely privy to all of what went wrong: the communications that failed, the successors who were lost, the rules that were ignored or wrongly executed, the little problem of nuclear weapons … and Putin.

Beyond problems with the succession, the events of 9/11 also exposed another weakness in the system. A senior official who had been the Pentagon’s continuity manager noted that if one of the hijacked planes had flown to the Capitol building, where Congress was in session, it could have led to constitutional crisis.

Under law, if a majority of congressmen and women were killed, the House of Representatives would not be able to deliberate because it would have lacked a quorum. And unlike the Senate, members of the House can only be released through a special election. The House, moreover, is charged with selecting a president if there is no available constitutional successor.

Who would have been in charge and what would have happened remains a nightmare that still drives close to a billion dollars a year in preparation just in case.

And as for the man who could have been king — Hastert — he entered the Federal Medical Center prison in Rochester, Minnesota, in June 2016.