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My father, John Joseph Judge was a WWII Army Air Corps veteran and had been a cryptographer assigned overseas. He worked as a civilian at the Pentagon after his return from the war until his death in 1965. My mother and my aunt both worked there as civilian employees beginning in 1943 until they retired. I grew up visiting the offices of my parents, and spending time at the Pentagon library. When the weather was nice, we would all often arrange to buy some food at the canteen and walk outside into the central courtyard area to sit and eat lunch together. When I was 10 or 11, to the best of my memory, which means 1957 or 58, I recall going outside and sitting down on a silver metal box. My father told me to get off of it. When I asked why he said it was a surface to air missile. (I could be off by 2-3 years on this recollection, but it was certainly before 1961).
It only makes sense that the Pentagon, especially in the years after WWII and the rise of the Cold War would have had air defenses built in. There were reports over the years in the local papers about such missiles. One was also reportedly installed on the White House lawn following the incident in 1994 when a small plane crashed just before hitting the building.
In 1998, I organized a demonstration for the War Resister's League to march from the National Cemetery to the Pentagon to demand "A Day Without the Pentagon", which was addressing what one-day of the Pentagon's budget could do in the civilian sector. In the course of getting a permit, I met with Col. Robinson, then a 30-year director of security at the Pentagon, who took me for a tour through the offices of the Joint Chiefs of Staff and then out to the parade ground beyond those offices where we were to end the march. He told me they were on Delta alert, their highest level of security alert and that they got bomb threats every day from Muslims. (In a larger meeting with security police from Metro, the Cemetery, the Arlington Police, the Pentagon and Washington, DC we were also asked if Muslims planned to join the march.) Col. Robinson then pointed to the roof of the Pentagon, just above us, and said, "And we have cameras and radar up there to make sure they don't try to run a plane into the building." That was a startling and almost non-sense statement to me in 1998, but recall that the method of attack and the target of the Pentagon were mentioned in the Bojinka Plan, retrieved from Ramsi Yusef's computer in the Philippines in 1996. Certainly they did not expect "cameras and radar" to stop the attacking plane, there was some method of defense coordinated with them (SAM's, interceptors, etc.).
And recall that in October of 2000, the Pentagon and the Arlington Fire Department ran an exercise for first response simulating a plane crashing into the courtyard. Many other sources confirm that they were anticipating such attacks using planes as weapons and prepared for that possibility (Senate/House Joint Intelligence Committee Report, NORAD's Amalgam Virgo II exercise, Secret Service preparations at the Genoa Summit in 2001, and FBI/CIA memos and conversations on Moussaui pre-9/11 that indicated he might "run a plane into the Twin Towers" or that he was a "potential suicide-hijacker" - see 9/11 Commission Final Report on these).
In addition to this I have two post-9/11 stories:
I cannot corroborate this, but someone at a public meeting told me that a friend who worked at the Pentagon said that a missile was fired on 9/11 from the Pentagon and that it struck Flight 77. If true, this might explain the FBI's reluctance to release the video footage they confiscated.
April Gallop, an enlisted member and survivor who worked at the Pentagon and brought her infant child to work that day, told me that when she was assigned there she got a classified tour of the building introducing her to its defenses, and she was told it was the best defended and safest building in the world. To this day she cannot comprehend why those defenses would have failed on 9/11.
And finally, the Pentagon sits inside the P-56-A restricted air space section that extends 17 miles in all directions from the Washington Monument, and that activated air defenses from a joint FAA/Secret Service radar and air traffic control at Langley, VA for many years prior to 9/11. Interceptor fighter jets in that area, which is separate from and more restricted than FAA commercial air space, as well as much better defended, were regularly scrambled when small or commercial planes went off course or were not on scheduled routes within a larger Air Defense Identification Zone (ADIZ) that extends 50 miles out to give time for the response. Andrews Air Force base, within 10 miles of the city as well as the 113th Air Wing of the National Guard at Anacostia NAS have provided consistent scramble-ready defenses for the P-56 sector, which protects the most important government buildings. Having grown up and lived in the area for most of my life, I saw such defensive responses many times, guiding planes away from the restricted area. Commercial pilots have also long complained about the difficult curving maneuvers necessary to land or take off at Washington National Airport (now Reagan) to avoid entering P-56-B, the three-mile inner restricted zone above the White House, Capitol and Pentagon.
These multiple layers of defense also inexplicably failed on 9/11 in the midst of a national crisis. Flight 77 was picked up by Langley entering the ADIZ according to the testimony of Mr. Mineta to the 9/11 Commission concerning a plane that was "50 miles out". That could only have been Flight 77, no others got that close, and the timing at 9:24-9:26 AM that he gives for the comment is also consistent with the timing of the impact. Neither was FAA/NORAD out of radar contact with the flight for more than a few minutes, since it was picked up by Indianapolis long before being seen by FAA ATC controllers in the DC area.