Response efforts after the Sept. 11, 2001 attacks were confused to the point that Vice President  Dick Cheney (search) mistakenly thought U.S. warplanes had shot down two hijacked aircraft, the Sept. 11 commission reported Thursday, the second and last day of its final public hearing.

The panel offered a dramatic retelling of the hour and 15 minutes that encapsulated the worst terrorist strike ever to take place on U.S. soil.

Some of the communications between air traffic controllers and the hijackers were played during Thursday's hearing.  One of the most chilling was from American Airlines Flight 11, which took off from Boston and was the first plane to strike the World Trade Center. 

The voice on that tape is believed to be that of Mohammed Atta (search), the alleged ringleader of the 19 hijackers, who piloted Flight 11 and is heard saying to passengers: "We have some planes. Just stay quiet and you'll be OK. We are returning to the airport."

Later, Atta tells the passengers: "If you try to make any moves, you'll endanger yourself and the airplane."

While it is customary for commission staff to read their report aloud, this one was augmented by snippets of tape recordings made that day as well as graphics demonstrating the flight paths of the four hijacked plans.

The panel is expected to make a final report next month on the events that killed nearly 3,000.

The panel met as President Bush personally disputed its day-old finding that there was no "collaborative relationship" between Saddam Hussein and the Al Qaeda terrorist network responsible for the attacks.

"There was a relationship between Iraq and Al Qaeda," the president said after a Cabinet meeting at the White House.

The dispute is a significant one, since Bush and top administration officials cited ties between Al Qaeda and the Iraqi dictator in the run-up to the invasion of Iraq in 2003.

Click to read the Sept. 11 Commission's report (pdf).

As for the response to the attacks, the front-line civilian and military agencies struggled to "improvise a homeland defense against an unprecedented challenge they had never encountered and had never trained to meet," the panel said.

"We fought many phantoms that day," Gen. Richard Myers (search), chairman of the Joint Chiefs of Staff, told the panel. He noted that reports of car bombings and other terrorist acts spread quickly — and falsely — in the frantic hours after the World Trade Center and Pentagon were struck by the planes.

The commission said efforts to respond to the four hijackings that day were plagued on multiple fronts.

Among them was difficulty in establishing secure communications between President Bush, who was in Florida at the time of the attack, and officials in Washington, the panel said.

"The president himself said in our interview with him how frustrated he was," said former Rep. Lee Hamilton, vice chairman of the panel. 

Some commissioners were sharply critical of the FAA. One, former Navy Secretary John Lehman, called its performance a "real inescapable failure." 

The commission said the military never received more than nine minutes notice from the FAA on any of the four hijackings.

Moreover, it added, there was a delay in passing along an order for pilots to shoot down any hostile aircraft. 

Additionally:

— The first call from the FAA to the military for help prompted a question: "Is this real-world or exercise?"

— One plane moved into a gap in FAA radar coverage.

— A single air traffic controller wound up with responsibility for two hijacked planes simultaneously.

— The FAA failed to notify the military that one of the four planes had been hijacked.

— The FAA incorrectly told the military that the first plane to crash into the World Trade Center was still in the air after impact.

The commission's report steered clear of any claims that the planes could have been intercepted. 

"NORAD (North American Air Defense Command) officials have maintained that they would have intercepted and shot down United 93. We are not so sure," the report said. That was the hijacked plane that crashed into the Pennsylvania countryside, evidently after passengers struggled with the terrorists aboard. 

"Their actions saved the lives of countless others," the panel said. 

In testimony before the panel, Gen. Ralph E. Eberhart, the NORAD commander, said that if the FAA had informed the military of the hijackings as soon as it learned of them, "yes, we could shoot down the airplanes."

It was a claim the commission did not second in its report. If FAA and NORAD officials were scrambling to deal with the strikes, so, too, were top officials of the government.

Cheney, in a secure, below-ground White House facility, received Bush's approval for pilots to shoot down aircraft deemed hostile. The vice president conveyed the order.

At midmorning, more than a half-hour after the order had been given, Cheney told Defense Secretary Donald H. Rumsfeld he thought it had been carried out.

"It's my understanding that they've already taken a couple of aircraft out," Cheney said, according to the partial transcript of a conference call that the commission released.

The report largely blamed inadequate emergency procedures that contemplated more time to react to a traditional hijacking rather than a suicide hijacking.

In many cases, the panel praised the actions of government personnel forced to make split-second decisions. In the hours just after the attacks occurred, nearly 4,500 planes in the air had to be landed as quickly as possible. To do that, air traffic controllers first had to reroute about a quarter of them — juggling 50 times the usual number of planes rerouted each hour.

"We do not believe that an accurate understanding of the events of that morning reflects discredit on the operational personnel," the report said.

The report said air traffic controllers realized at 8:24 a.m. on Sept. 11 that Flight 11 was being hijacked, but lost several minutes notifying layers of command — according to protocol — before contacting NORAD. The plane crashed at 8:46 a.m.

Controllers, meanwhile, didn't realize American Airlines Flight 77 — which took off from Dulles Airport outside Washington — might be hijacked when it mysteriously started veering off course at 8:54 a.m. The plane then traveled undetected for 36 minutes toward Washington, due in part to a radar glitch.

The confusion meant only an unarmed military cargo plane could be diverted to track the plane. The plane located Flight 77 but its crew could do nothing as the commercial jetliner crashed into the Pentagon.

The Associated Press contributed to this report.