One of the most important parts of the official story is that the government couldn't track the location of the hijacked planes because the hijackers had turned the transponders off. The official version is that, with transponders turned off, only "primary radar" was available to civilian air traffic controllers. Primary radar can track location, but not altitude.

This makes no sense, because America's air defenses need to protect our nation against foreign fighter jets and other airplanes invading our country. Is our trillion-dollar defense system set up so that a Russian or Chinese pilot can invade undetected if he just turns off his transponder? Darn! Why didn't we think of that?!

Primary radar is a red herring.

Why?

Because the military possesses highly sensitive radar. For example, "military radar can track space debris as small as 10 centimetres across" miles up in space.

AWACS Should Have Tracked Planes

Airplanes known as AWACS have incredibly sensitive Doppler radar that can detect any moving object. As an Army website states:
 

"Although Airborne Early Warning and Control System (AWACS) airborne radar can detect practically any moving object, aircraft radar operators routinely screen out objects moving slower than 85 miles per hour to avoid tracking motor vehicles."

There was, in fact, at least one AWACS near Washington, D.C. on the morning of 9/11 participating in a war game exercise. The pilot learned of the attacks soon after the first hit on the World Trade Center. While, at first he thought it was part of the war game exercise, "it didn't take him long to realize it was real."

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The military should have had the pilot track all planes moving in and around the White House-Pentagon corridor. That would have been standard military protocol: to protect the command and control structure of the U.S. government and military.

The Pentagon-White House Corridor Is Highly-Monitored

Even if AWACS pilots were not instructed to monitor the area, the Pentagon and White House are two of the most heavily-defended buildings in the world. They are only 2 miles apart, and the entire area is protected air space (because the area is home to the seat of power of the commander in chief and the military) and - because there have been numerous incidents of planes approaching the White House - it is entirely certain that the whole area is covered by very sophisticated military radar.

And keep in mind that installing military radar on the ground is much easier and less expensive than mounting it in a moving airplane.

Andrews Air Force Base is only 10 miles from the Pentagon, and has doppler radar even for public weather monitoring (if the base has doppler for something as mundane as weather monitoring, doesn't it make sense that the air force base closest to the Pentagon and White House would have sophisticated radar to protect the White House and Pentagon? Or do they just monitor the weather?)

The Pentagon itself also has access to the highly sophisticated PAVE PAWS radar which is capable of monitoring many planes or missiles simultaneously.

Indeed, this CBS news article implies that military radar actually was tracking Flight 77 as it approached the Pentagon. And Dick Cheney -- sitting in a military command bunker underneath the White House-- monitored flight 77 for many miles as it approached the Pentagon (confirmed here).

The Other Planes

While I have focused on Flight 77 and the area surrounding the Pentagon, this diagram shows that all of the hijacked planes flew over numerous military bases on 9/11 before crashing. Those military bases undoubtedly possess highly-sophisticated radar as well.

In addition, the is strong evidence that the planes were being tracked. For example, an ABC News article states:
 

"Controllers at the Boston Center knew American Airlines Flight 11, which departed at 7:59 a.m. ET from Boston for its flight to Los Angeles, was hijacked 30 minutes before it crashed. They tracked it to New York on their radar scopes. 'I watched the target of American 11 the whole way down,' said Boston controller Mark Hodgkins. "
 

Similarly, air traffic controllers and others tracked Flight 175.

Confirmed

All of the above-described information confirms the statement by a former air traffic controller, who knows the flight corridor which the two planes which hit the Twin Towers flew "like the back of my hand", and who handled two actual hijackings, that planes can be tracked on radar even when their transponders are turned off (also, listen to this interview).