By Lisa Myers Senior investigative correspondent
NBC News
updated 7/21/2004 7:07:42 PM ET 2004-07-21T23:07:42

On Thursday, the bipartisan 9/11 commission issues its final report, wrapping up a nearly two-year probe into the events that led to the worst act of terrorism in U.S. history. The commission will conclude that there were dozens of missed opportunities, clues that went undetected and crucial pieces of intelligence that America's counterterrorism investigators simply failed to share with one another.

This is an attempt to step back and examine all those missed chances, the tiny puzzle pieces that, sadly, were never assembled in time.

On Sept. 11, 2001, the attacks seemed to come from out of the blue. They were sudden, horrifying and without warning. But almost three years later, the picture has changed dramatically. Two investigations have concluded that the attacks, while shocking, were not completely unforeseeable. And the trail of missed clues and missed opportunities to stop some of the hijackers, disrupt the plot or perhaps save 3,000 lives stretches across continents.

"We sounded an alarm. We knew the threat was lethal, unambiguous and started here. … We knew it was coming at us. We put our hearts and our souls into disrupting and preventing those attacks.  We did all we knew how to do, and we failed."

That was the testimony of CIA Deputy Director of Operation James L. Pavitt before the 9/11 commission in April 2004.

The commission's final report acknowledges that the nation's counterterrorism warriors tried to defend America from attack, with some successes. But the cold truth is that their legacy will be failure on a massive scale.

Infiltrating the enemy
As early as 1996, Osama bin Laden made clear his intentions, issuing a 60-page “fatwa” declaring war against the "American enemy." He was training more than 10,000 foreign fighters at his camps in Afghanistan and even readying young children as the next wave.

Despite the constant stream of freshmen recruits schooled in Afghanistan in terror tactics, America’s CIA failed to infiltrate al-Qaida's top ranks. Former CIA Director George Tenet told the commission, "We ran over 70 sources and subsources, 25 of whom operated inside of Afghanistan. …  However, we never penetrated the 9/11 plot overseas."

In the fall of 1999, bin Laden and his aides began secretly planning the 9/11 attacks. 

The Malaysia meeting
In January 2000, al-Qaida's top operatives converged on Kuala Lampur for what's known as the "Malaysia meeting.” Suicide operatives Nawaf al-Hazmi and Khalid  al-Midhar, both Saudis, arrived for a 9/11 planning meeting, handpicked by bin Laden. This was the first time any of the hijackers appeared on the radar of American intelligence.

The CIA successfully tracked al-Midhar to the meeting. As he and his al-Qaida conspirators convened inside a safehouse, local spies kept watch outside. But the CIA failed to bug the building and lost bin Laden's handpicked terrorists altogether when they left Kuala Lampur for Thailand.

At this point, the CIA knew  al-Midhar had a valid visa to enter the United States, but it failed to inform the FBI or to place the terrorist on a U.S. government watch list. Commission members keyed in on this oversight at an April 2004 hearing.

"To me that's like a sheriff in a local town finding some people on the border of Indiana that are suspected murderers, letting them go across the border in Michigan and not alerting anybody that they're on their way," said 9/11 commissioner Tim Roemer.

Jamie Gorelick agreed, saying, "You knew that Midhar had a U.S. visa. And so my question is, why at that point was he not put on the tip-off watch list?"

"Well, I would say that particular case should have been," said former CIA official Cofer Black. "In fact, I would say that there were multiple opportunities where we could have watch-listed."

On Jan. 15, 2000, al-Midhar and al-Hazmi flew to Los Angeles. They were the first two 9/11 hijackers to enter the country for the mission. It would be 19 months before the CIA warned the FBI that the two terrorists might be in the country.

The calls
Then, phone calls came from halfway around the globe, in Yemen. The super-secret National Security Agency was monitoring a Yemen house around the clock. Inside was a so-called al-Qaida switchboard, which received calls from bin Laden and relayed messages to his operatives around the world.It was run by Samir al-Hada, Khalid al-Midhar's brother-in-law.

Investigators tell NBC News that in early 2000, days after the two hijackers settled into a San Diego apartment, al-Midhar got the first of what would be a dozen calls from the switchboard in Yemen.

The NSA intercepted the calls and knew they were to someone named Khalid. But it failed to detect the crucial fact that this known terrorist facility was calling someone inside the United States.

The NSA had the technical ability to pick up the actual phone number in the United States that the switchboard was calling, but didn't deploy that equipment, fearing it would be accused of domestic spying.

"It's a failure to recognize how important Yemen is to the al-Qaida network," says NBC News analyst and terrorism expert Roger Cressey.

The final call from Yemen to the hijackers came only weeks before 9/11.

The walk-in
In April 2000, Niaz Khan, a down-and-out Pakistani from Britain who had arrived days earlier at New York's JFK airport, told the FBI an incredible story. Khan says he was recruited by al-Qaida, trained in Pakistan to hijack planes and sent to the United States, where he was supposed to meet five or six people — some of them pilots — for an undisclosed terror mission. But once in the United States, Khan got cold feet. 

"I told them before 9/11, about more than year, be hijacking in America or on [an] America airline," Khan says.

The FBI confirms Khan passed two polygraphs. Still, FBI headquarters didn't believe him and sent him home to London. The FBI insists it investigated Khan's story thoroughly, but acknowledges it did not share his information with the CIA, nor take Khan up on his offer to return to Pakistan with investigators to try to find the terrorist training site, the house where he was trained.

Four years later, U.S. intelligence has concluded Khan was credible despite doubts by the FBI.

"That's part of the systematic failure of the bureau to seriously deal with the al-Qaida threat inside the U.S. before 9/11," says Cressey.

In June 2000, ringleader Mohammed Atta entered the United States and enrolled in flight school in Florida.

The sighting
Back in Afghanistan, the preparations for 9/11 picked up in pace. In a rarely seen al-Qaida-produced videotape, terrorists who would later hijack three of the four doomed airlines gathered at an Afghanistan hideout. On the wall behind them was a crudely drawn targeting map of the United States, adorned with a cartoon image of a bomb.

In the fall of 2000, in the mountains of Afghanistan, an unmanned Predator spy drone flew over known al-Qaida training camps and captured extraordinary pictures, including a tall figure in flowing white robes. The CIA believed then and now it was Osama bin Laden. The pictures were fed live to the CIA and were the best real-time information U.S. intelligence ever had on bin Laden's whereabouts.

"This was the equivalent of having bin Laden in the crosshairs," says NBC News analyst and terrorism expert Steve Emerson.

But the United States was not prepared. There were no military assets in place to even attempt a strike on bin Laden.

"We should have had strike forces prepared to go in and react to this intelligence, certainly cruise missiles either air- or sea-launched — very, very accurate — they could have gone in and hit those targets," says NBC News analyst Gen. Wayne Downing (ret.).

The 'chatter'
In the following months, from the safety of Afghanistan, bin Laden personally managed the 9/11 plot. By the summer of 2001, investigators say word spread through the jihadist community of an imminent attack on the United States. At one of his camps, bin Laden urged trainees to pray for the success of a coming attack involving 20 martyrs.

In the United States, between May and July 2001, the NSA, which eavesdrops on communications around the world, reported 33 messages that suggested "a possibly imminent terrorist attack," according to a congressional investigation.

In May, an intelligence report indicated al-Qaida operatives were planning to infiltrate the United States to carry out an attack using explosives. In June, a CIA report said important bin Laden operatives were "disappearing." Others were preparing for "martyrdom." 

"We have people in Washington, the CIA director and others, saying their hair was on fire, this is a spike in warnings," said commissioner Roemer.

The false documents
By June of 2001, all 19 hijackers had entered the United States, entering a total of 33 times through 10 airports.

Despite previous claims by the FBI and CIA that all the hijackers were in the United States legally, the 9/11 commission found as many as 11 had doctored passports or told easily detectable lies on their visa applications and should not have been allowed into this country.

"The 9/11 hijackers included among them known al-Qaida operatives who could have been watch-listed, presented passports manipulated in a fraudulent manner or presented passports with suspicious indicators of extremism," commission staff director Phil Kelikow said at a Jan. 26 hearing.

Even 9/11 mastermind Khalid Sheikh Mohammed was granted a visa to enter the United States weeks before the attacks, despite the fact that he'd been indicted for terrorism five years earlier and should not have been able to get a U.S. visa.  Investigators do not believe he actually entered the country.

"It’s probably the most graphic example of the inability to share information inside the federal government," says Cressey.

The Phoenix memo
On July 10, 2001, Phoenix FBI counterterror agent Ken Williams sent headquarters a prophetic memo warning of "the possibility of a coordinated effort by Osama bin Laden to send students" to U.S. flight schools. He listed an "inordinate number" of Muslim extremists training in Arizona flight schools and urged the FBI to canvas other cities.

The FBI failed to act. The memo generated little interest and was dismissed as speculative.

"It was looked at there. It was analyzed," said former FBI director Louis Freeh at an April 13 commission hearing. "People took what they thought was the appropriate action at the time."

"I think had it gotten into the works up to the highest possible level, at the very least 19 guys wouldn't have got on to these airplanes with room to spare," 9/11 commission member and former Democratic Sen. Bob Kerrey said at the same hearing.

On Aug. 6, President Bush received an intelligence briefing he requested on the possibility of al-Qaida attacking inside the United States.

Titled, "Bin Laden Determined to Strike in U.S.", the presidential daily briefing included intelligence on various al-Qaida plots against the United States, including one in 1998 in which bin Laden wanted to hijack a plane to gain the release of an extremist radical sheik.

However, the CIA said in the memo, "We have not been able to corroborate some of the more sensational threat reporting."

"All the king's horses and all the king's men in the CIA could not corroborate what turned out to be true," said commission member and former Navy secretary John Lehman.

"If this is the way the intelligence filters up, we have a serious problem, because none of the important details ever filtered up to the president," says Emerson.

The Moussaoui arrest
On Aug. 16, 2001, the FBI arrested suspected terrorist Zacarias Moussaoui, who was training at a flight school in Minnesota.

"As the FBI was communicating it that day to the CIA and the FBI referred to Moussaoui as "suspected suicide attacker" planning to fly a commercial airliner in the United States of America.  Suspected suicide hijacker," said Democratic commission member and former Watergate prosecutor Richard Ben-Veniste.

Yet, FBI agents were denied a warrant to search Moussaoui's computer and other belongings, forcing a frustrated supervisor to sound a stunning warning to headquarters.

"On Aug. 27, the FBI supervisor in Minneapolis, trying to get the attention of those in headquarters at FBI, said he was trying to make sure that Moussaoui, and I quote, ‘Did not take control of a plane and fly it into the World Trade Center,’" said Ben-Veniste.

Information on Moussaoui's arrest never made its way up the FBI chain of command. When did acting director Tom Pickard finally hear of it?

"That was about 3:00 in the afternoon, Sept. 11," said Pickard at an April 14 commission hearing.

At the CIA, the Moussaoui arrest was treated more urgently.  Still, when Director George Tenet was informed later that month, the briefing was benignly titled "Islamic Extremist Learns to Fly."

Why didn't Tenet immediately alert the President?  "I didn't see the president," said Pickard. "I was not in briefings with him during this time."

Investigators would eventually search Moussaoui's belongings after Sept. 11. They connected him to al-Qaida and to planners of the 9/11 plot.

"The Moussaoui episode is one of the top three examples of where we might have been able to stop 9/11," says Cressey.

The search
On Aug. 23, less than three weeks before the attack, the CIA finally told the FBI that Khalid al-Midhar and Nawaf al-Hamzi may be in the U.S. and put them on most government watch lists.

But investigators say the FBI conducted an inept investigation and failed to locate either hijacker, even though they had their names listed in the San Diego phone book and were living in an apartment.

An FBI agent testifying incognito told congressional investigators he wanted to go after al-Midhar more aggressively, but was shot down by headquarters, which said there was no criminal case.

"I wrote on Aug. 29, 2001, ‘Whatever has happened to this, someone, some day, someone will die — and the public will not understand why we were not more effective,’" said the agent.

Another agent lamented there were never enough FBI agents to follow all the al-Qaida leads.

"There are also the kinds of misses that happen when people, even very confident, dedicated people are simply overwhelmed," said the other agent.

It's become urban legend that the 9/11 hijackers kept to themselves and shied away from other extremists.  But 9/11 investigators now know that the hijackers met frequently with other U.S.-based Islamic extremists.  In fact, the hijackers had contact with 14 people known to the FBI prior to 9/11 as a result of other counterterrorism investigations.  

"Rather than the hijackers being invisible to the FBI they were in fact right in the middle of the FBI's counterterrorism coverage and yet the FBI didn't detect them," said commission staff director Eleanor Hill.

Case in point, two of the hijackers were living in San Diego with an undercover informant for the FBI.

"There was nothing in their interaction that would give any indication that these two were in the U.S. to commit a terrorist act," said FBI director Robert Mueller.

The watch lists
Even though al-Hazmi and al-Midhar were put on the State Department watchlist in late August, they were not put on the Federal Aviation Administration’s "no fly" list.  That would have kept them from boarding flight 77, which crashed into the Pentagon.

They weren't banned from flying because the FAA only put terrorists on the "no fly" list who were known to be interested in hijacking planes.

Commission member Slade Gorton: "Merely being a suspected terrorist doesn't get you on that no-fly list?"

Assistant administrator for Intelligence, Transportation Security Administration, Claudio Manno: "It can; it depends what group you're associated with and what other information there is."

Gorton:"Wow, I find that to be an incredible answer."

Airport security
The hijackers did trial runs to see what weapons they could get through airport security checkpoints. Their preparation paid off.

FAA and industry guidelines banned passengers from carrying box cutters and knives with blades of 4 inches or longer. But blades of less than 4 inches were allowed if screeners didn't consider them menacing.

"Nobody should be allowed on an airplane with a knife that has a blade you could cut wood with," says Ron Motley, a lawyer for 9/11 families.  "Nobody should be allowed on an airplane with a box cutter."

But the hijackers managed to sneak on box cutters and investigators say they almost certainly used knives like "Leathermans" — the utility knife discovered in the wreckage of the plane that crashed in Pennsylvania.

At Dulles airport, three of the five hijackers who passed through checkpoints set off the metal detectors a total of five times. The three were rescreened, two with handheld wands, and passed.

"They counted on beating a weak system," said commission member Bill Johnstone.

One of the last lines of defense, the airport security system and the screeners, also failed that day.

"They were zero for 19," says Motley. "Nineteen dangerous people got on four different airplanes, cut the throats of passengers and crews and were able to take control of the airplanes."

Air defenses
Sept. 11, 2001, was a brilliant day in the East.

The first ominous sign, at 8:24 a.m., came from American Flight 11 from Boston.  A hijacker, believed to be Mohammed Atta, thought he was talking to passengers, but keyed the wrong microphone and spoke to FAA controllers instead.

Atta: "We have some planes. Just stay quiet and you'll be OK. We are returning to the airport. Nobody move.  Everything will be OK. If you try to make any moves, you'll endanger yourself and the airplane. Just stay quiet."

At 8:37 a.m., the FAA finally informed the military of the hijacking, but by the time jets scrambled, it was too late. At 8:46 a.m., the first plane hit.

Audiotapes reveal that for the next crucial minutes, federal agencies that were supposed to protect the public were crippled by confusion, chaos and indecision.

FAA command center: "Do we want to think about scrambling aircraft?

FAA headquarters: "God, I don’t know."

FAA command center: "That's a decision somebody's going to have to make, probably in the next 10 minutes."

FAA headquarters: "You know, everybody just left the room."

The FAA repeatedly failed to alert the military's air defense system, NORAD, of the hijackings in a timely manner, eliminating any chance of intercepting some of the planes before they could crash into buildings.  Nine minutes' notice was the most the military got before any of the hijacked planes crashed.  In one case, the FAA didn't tell the military at all.

"I think headquarters blew it," says Bob Kerrey. "I mean, there was no information delivered to the military that a plane was coming into Washington, D.C.  And I thank God the passengers on 93 took the plane over."

"We only had 14 airplanes on alert, seven alert sites," said Gen. Ed Eberhardt, commander of the U.S. Northern Command, at a June 17 hearing.

When F-16s did manage to scramble, some went the wrong direction, out to sea. Pilots weren't even told it was hijacked planes they were looking for. So, when one pilot saw the Pentagon in flames, he instantly blamed the Russians, saying, "I'm thinking cruise missile from the sea.  I thought the bastards snuck one by us."

But it was a newer, more nimble enemy who "snuck one by us." How al-Qaida could pull off such a devastating sneak attack comes into focus now, with three years of hindsight, investigation and clues that leap out in retrospect, but were much harder to recognize in the pre-9/11 world.

"If you look at the details of what these 19 men did on 11 September, they defeated every defense that we had in place, every single one of them," says Kerrey. "And there is no other word that you can put on it other than they defeated us."

"Would you expect them to be prepared for the totally ingenious evil attack and the way it was performed? No," says commission Chairman Thomas Kean, a former New Jersey governor. "Should they have been more ready for something coming? Yes."

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