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America's armed forces prepare and train every day to defend the country from the worst threats imaginable.

But on Sept. 11, the worst happened.

"We were in the middle of a North American Air Defense Command exercise," said Gen. Larry Arnold, a recently retired commander of the North American Aerospace Defense Command (NORAD).

Air troops were readying for a day of war games.

But then the phone rang at Florida's Tyndall Air Force Base.

It was the Federal Aviation Administration (FAA), asking for an escort for a hijacked plane. They heard reports of a possible stabbing of a flight attendant.

This was no drill. It was real. But no one could find the plane.

It was "horribly frustrating to know there is something in there...but I don't have any eyes," said Lt. Col. Dawn Deskins of the NE Air Defense Sector. "He [FAA] gave me the latitude and longitude of that track …[but] there was nothing there."

NORAD's radar system was built during the Cold War to watch out for Soviet bombers or missiles. It was never intended to monitor commercial jets over the United States. That job belongs to the FAA.

"We didn't know how many more of those hijackers there were...whether it was four...five...six or seven," added Lt. Col. William Glover, commander of the

Air Warning Center in Cheyenne Mountain, Col.

America’s air defense forces were trying to down a hijacked airliner they could not see. The only information coming was from the FAA over the telephone.

A call then went out to Otis Air Force Base in Cape Cod, Mass., with orders to get fighter pilots Maj. Dan Nash and Lt. Col. Timothy Duffy into their F-15s and in to the air — in a hurry.

"When you get the scramble order…you are usually not sure what is going on," Duffy said.

"But when we heard it was a hijacking … we knew it was the real thing," Nash added.

The pilots flew to New York, but didn’t know they were already too late. Television gave them what their radar could not: a view of what was going on in Lower Manhattan.

"I remember a young troop coming into the battle cab … with an ashen face, saying ... 'Sir, the World Trade Center has been hit. The news is reporting that an airliner crashed into the World Trade Center,'" said Col. Robert Marr, commander of the Northeast Air Defense Sector.

Word then came that a second hijacked airliner, United Flight 175, was screaming toward New York. Nash and Duffy were still 70 miles away from the city when the second tower was struck. That’s when NORAD knew America was under attack.

"We were going to intercept a hijacked aircraft but nobody expected to happen what happened," Nash said. "I was in shock and really pissed off."

As the towers burned and more than 4,000 airliners were flying the U.S. skies, NORAD feared more hijacked planes may be heading toward New York. And the only two fighter jets defending the city were low on fuel. The next nearest ones were at Langley Air Force Base in southern Virginia.

There, Maj. Dean Eckman and Maj. Brad Derrig suited up and got into their jets. NORAD got word from the FAA that American Airlines Flight 77 had taken off from Dulles International Airport in Washington, headed west, but was no longer in contact.

The Langley pilots were ordered to defend the nation’s capitol. Although they sped to the scene at 700 mph, Eckman and Derrig arrived minutes too late.

"One of the guys … we got a bit closer … made the comment … 'Hey, that is the Pentagon on fire,'" Derrig said.

The fighter pilots were unaware that a fourth hijacked plane, United Airlines flight 93, nearing Cleveland, Ohio, had turned and headed toward Washington. Cleveland air traffic controllers couldn’t make contact with the plane.

The order came from the White House to "shoot it down."

"The word that came down the secure line was … almost verbatim … 'we will take lives in the air to preserve lives on the ground,'" Marr said.

But then, the passengers of Flight 93 made their last stand and assumedly rushed the cockpit and fought with their hijackers, eventually driving the plane into the ground in rural southwest Pennsylvania.

Meanwhile, Duffy and Nash were flying around New York escorting planes to airports. After the south tower collapsed, they flew over to the site just as the north tower came down.

"All of a sudden, it started falling away from me," Duffy said. "My first thought as I saw the building going down was the firefighters … it occurred to me that they would be running into it when everyone else was running out."

Shortly after noon east coast time that day, the nation’s skies were empty — all except for the pilots who had front row seats to one of the nation’s darkest days.

"I look at it as my generation’s Pearl Harbor," Eckman said. "I was witness to a huge historical event … that hopefully we will never see repeated again."

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The U.S. military has had to quickly adapt to fight a new enemy here at home.

"Our great frustration is...'Why could we not have been there to stop such an attack?'’" said Sgt. Rhonda Hees of the SE Air Defense Sector of NORAD.

In a sense, American was fortunate there were just four hijacked jets, because that day, the nation’s military had just 14 fighter jets to defend the entire country. But that has all since changed.

"We have far more fighters available to fly missions in the United States and Canada," said Brig. Gen. J.D. Hunter, vice commander of the Cheyenne Mountain Operations Center, the nerve center of NORAD. But just how many more is a secret.

"I can’t tell you where we have fighters on alert … or what status they are on … or how often we put fighters in the air...but just recognize that our ability to respond is much...much quicker now," Marr said.

NORAD now has a map of the continental United States showing every commercial airliner that has filed a flight plan with the FAA. The green dots symbolize an airliner. With a single mouse click, the military can check and see if the plane is on its correct flight path.

"We have connected to over 50 radars in the interior U-S that gives us the ability to look at the picture...the same picture that the FAA's looking at...at the same time," Glover said.

But the FAA radar does not cover every mile of the United States and it doesn’t track every plane.

"I'm not going to pretend to say that I see every aircraft that is in the air all the time," Marr said.

Those radar coverage holes came into play on Sept. 11. One year later, there are still places where radar does not reach.

But compared to what they were looking at on Sept. 11, the view of America’s skies is much improved, and so is the communication with the FAA.

FAA representatives are often now found in the NORAD command center where all of the radar and communications equipment is located. The military now monitors FAA communications. If there's a problem in the sky, NORAD will have a jump on the situation.

"We have better air defense," Arnold said. "We have better radar coverage."

There may not be a perfect defense strategy for protecting the homeland. But America's defenders say America is a safer place now than it was on Sept. 11.

"There is no doubt that we are more secure in the air," Marr said.

Fox News’ Liza Porteus contributed to this report.