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PAULA ZAHN, CNN ANCHOR: And we are now just beginning to learn more and more about what led to 9/11 and how it played out with air traffic controllers. Go into an air traffic control center today you will see row after row of very dedicated very intense people starring at blips on a screen, and calmly, surely moving them around the sky.
Now, each blip represents hundreds of lives, each controller handles dozens of blips a day, and remarkable enough, in the best of times, in the worst of times, even better.
Miles O'Brien has their story
MILES O'BRIEN, CNN ANCHOR: Stroke by stroke, the hijackers painted a diagram of their evil plot on radar screens in air traffic control centers in New Hampshire, Ohio, New York and Virginia that morning, but it happened too quickly and in too many places for controllers to see the synchronicity as it unfolded. The fog of war had enveloped air traffic control.
The first came at about 8:15, when a controller cleared American Airlines flight 11 to climb from 29,000 to 35,000 feet.
GLENN MICHAEL, AIR TRAFFIC CONTROLLER: There was no acknowledgment from the pilot on that transmission. Further attempts by our controllers to contact American 11 were fruitless. We never re-established contact with the aircraft.
O'BRIEN: American 11's transponder, which transmits altitude and airspeed, went silent. The controllers heard a stray radio call. We've got planes, declared the voice. It now seemed obvious this was a hijacking. They responded as they were trained.
LINDA SCHUESSLER, AIR TRAFFIC CONTROLLER: From the air traffic perspective, the handling of the hijack would be whatever the aircraft needs or want, we would give it to them.
O'BRIEN: At 8:40, controllers picked up this he phone to notify NORAD. One minute later, a controller in the tower at Newark Airport cleared United flight 93 for takeoff. 93's flight path crosses United 175's, although its transponder was still on, it had seized talking to controllers. At 8:43 New York controllers made their call to NORAD.
Three minutes later, American 11 hit the north tower. Controllers in the New York terminal radar approach facility, or TRACON, tracked united 175 as it turned left over New York harbor toward lower Manhattan.
MICHAEL MCCORMICK, AIR TRAFFIC CONTROLLER: Probably one of the most difficult moments of my life was the 11 minutes from the point I watched that aircraft when we first saw these communications on to point that aircraft hit the World Trade Center. For those 11 minutes, I knew, we knew, what was going to happen.
O'BRIEN (on camera): In Newark Tower, they could see the plane make its ominous turn. They watched in horror as the tragedy unfolded. With the World Trade Center in flames, controllers threw out their old hijacking playbook an started making up some new rules. Two minutes after the second tower was struck, Boston sector banned all departures in its sector. Two minutes later, 9:06 a.m., Boston, Cleveland and Washington banned all departures of flights headed toward New York.
Then two minute later, at 9:08, New York slams the door entirely, banning all flights headed its way.
(voice-over): In Oberlin, Ohio, at the on-route facility known as Cleveland center, things got busy very quickly. Controllers began holding dozens of New York-bound planes in their airspace, while looking for the signs of more trouble.
RICK KETELI, AIR TRAFFIC CONTROLLER: That's where Delta 1989 came in.
O'BRIEN: Delta 1989 hit the terror profile. A 757, it left Boston bound for Los Angeles only five minutes behind United 175.
KETELI: He told the controllers not to share what they knew, because at that point, folks had seen the aircraft hit the Trade Tower, obviously, in the cafeteria, where our television is located, and they knew pretty much things were pretty extraordinary.
O'BRIEN: Meanwhile, United flight 93 appeared on radar screens here. The first call from the pilot, routine. Controllers remember him sounding cheerful, and then at 9:32, they heard the first of four troubling radio transmissions.
KETELI: The first transmission that sounded like struggle in the cockpit. It was pretty clear, then we had a second transmission also that was a struggle in the cockpit, and you could hear the pilots, what appear to be the pilots, yelling "get out, get out!" and a lot of -- and the other noise that appeared to be a struggle.
O'BRIEN: At first, they suspected it was delta 1989, and their fears grew when it asked to land in Cleveland. As it turns out, the crew was ordered to land by the airline. Before controllers could check, though, their radar screens pointed them in a different direction. It was United 93 that had abruptly descended, and then climbed to 41,000 feet without approval.
KETELI: The information traveled through the control room with lightning speed and everybody kind of took a deep breath and realized, wow, we're part of this, too. There was no doubt what we were dealing with.
O'BRIEN: By now, controllers in Washington center were dealing with their own unresponsive airplane. American 77 departed Dulles for Los Angeles at 8:21, just as American 11 had stopped talking to controllers. The plane flew as far west as Indiana, and then took a U-turn toward the heart of the nation's capital.
(on camera): It crashed at 9:40. Five minutes later, at the FAA command center in Herndon, Virginia, they made a stunning, unprecedented decision, clear the skies, have every aircraft over the continental United States on the ground as quickly as possible, and there were more than 6,000 aircraft to deal with at that moment. There were no procedures for us this. No one had contemplated, much less practiced, such a scenario.
HATFIELD: We started giving pilots options at the closest airport and started landing those aircraft.
O'BRIEN: As that order came down, United 93 was heading southeast toward Washington, its altitude reporting transponder silent. Controllers heard a pair of radio calls, which sounded like P.A. announcements. "We have a bomb," they claimed.
KETELI: The aircraft turned abruptly to the east, and then hard right turned abruptly to the south, due south, and then eventually disappeared from the radar.
O'BRIEN: It was 10:07. Controllers were focus on emptying the skies, offering little explanation to incredulous pilots.
HATFIELD: We asked them to make sure their cockpits were secure. and We solicited the airport of intended landing. That is all.
O'BRIEN: By 12:15, two and a half hours after the order was issued, four hours after the hijacking of American Airlines flight 1 1, the airspace over the continental U.S. was cleared. Only military and emergency aircraft were in the air now.
(on camera): Is it your hunch, your conviction, whatever, that there were planes that were thwarted by the FAA?
MIKE MCCORMICK, AIR TRAFFIC CONTROLLER: I don't think it could ever be proven. However, I feel very comfortable in the knowledge that the knowledge that the air traffic controllers were the heroes that first rose to the defense of our country on September 11th, and the decision to remove the weapons of destruction from terrorist in that attack, in fact, saved many lives, and there were other opportunities and there were other plans that we intervened.
O'BRIEN: We may never know for sure, but after that brutal, breath-taking morning, a silent sky what is the nation needed that afternoon.
Miles O'Brien, CNN.
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