TIME Exclusive: Inside the Plot
In an excerpt from TIME's forthcoming special issue, TIME's exclusive reporting on the terror in the sky and the plotting on the ground. 

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Wednesday, Sep. 12, 2001
Only God knows what kind of heroic acts took place at 25,000 feet as passengers and crews contended with four teams of highly trained enemy terrorists. But it is clear that the hunt for the culprits began way up in the sky, by the doomed passengers and crews themselves, minutes before the attacks took place. The victims on board at least two of the four planes whispered the number and even some of the seat assignments of the terrorists along with their final goodbyes in their brief and haunting Tuesday morning cell phone calls. A flight attendant on board American Flight 11 called her airline's flight operations center in Dallas on a special airlink line and reported that passengers were being stabbed.

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That gave investigators a head start Tuesday morning that something had gone terribly wrong, but there were plenty of other clues. Even before the smoke had cleared, it was obvious that the culprits knew their way around a Boeing cockpit - and all the security weaknesses in the U.S. civil aviation system. The enemy had chosen the quietest day of the week for the operation, when there would be fewer passengers to subdue; they had boarded westbound transcontinental flights - planes fully loaded with kerosene; armed with makeshift knives and retractable knives; they had gained access to the cockpits and herded everyone to the back of the plane. Once there, they turned off the aircraft's self-identifying beacons known as transponders, a move which renders the planes somewhat less visible to air traffic controllers. And each aircraft performed dramatic but carefully executed course corrections, including a stunning last maneuver by flight 77. The pilot of that plane came in low from the south of the Pentagon and pulled a 270-degree turn before slamming into the west wall of the building.

The hunt for those responsible

By Tuesday afternoon, the spooks were making progress. Eavesdroppers at the supersecret National Security Agency had picked up at least two electronic intercepts indicating the terrorists had ties to bin Laden. By nightfall, less than 12 hours after the attacks, US officials told TIME that their sense that he was involved had gotten closer to what one senior official said was 90 percent. The next morning, US officials told TIME they have evidence that each of the four terrorist teams had a certified pilot with them, some of whom had flown for Saudi Airlines. It?s not yet clear whether the pilots were trained in the US, or in Saudi Arabia or both. Intelligence officials believe each team had four to five persons. Some team members, it is thought by US intelligence, crossed the Canadian border to get into the U.S. TIME has learned that within the past few months, the FBI placed two men associated with an Islamic Jihad terror group on a border watch list, but through a screwup, the pair got into the U.S. anyway. The two men appear to have been on American Airlines Flight 77, the plane that crashed into the Pentagon, TIME has learned. Boston appears to have been a central hub for the operation; U.S. intelligence believes a bin Laden cell in Florida was a support group helping with the aviation aspects of the attack.

Intelligence officials pouring over old reports believe they got their first inkling of planning for the attack last June, although at the time the intelligence was too vague to indicate the scale of the operation. In the summer U.S. embassies, particularly those in the Middle East, were put on heightened alert. The U.S. military in the region moved to a higher level of alert. The CIA was getting vague reports "of some kind of spectacular happenings" by terrorists, said a U.S. intelligence official, but the reports were vague as to timing. "A lot of this reporting we had in the summer that gained our attention and had us concerned, but wasn't specific, could have been tied to this," said U.S. intelligence officials.

Even had they known more, could officials ever have contemplated the scale of this thing? The blasts were so powerful that counter-terrorism teams have begun asking the airlines for fuel loads on the plane; aviation experts have been asked to calculate the explosive yield of each blast -in kiloton terms. The reason? Washington wants to see if the planes amounted to weapons of mass destruction. "What we want people to realize is they?ve crossed a line here," said a U.S. intelligence official. In fact, some senior administration officials are considering drafting a declaration of war, although the State Department is leery since nobody knows precisely who the war would be against.

Placing the blame

"Anyone who says this is not an intelligence failure is blowing smoke. This is an intelligence failure and a security failure," said Lt. Gen. (ret.) William Odom, former head of the National Security Agency (NSA) and the former head of US Army intelligence. "The security guys will blame it on the intelligence guys and the intelligence guys will tell us the great successes they had in the past."