Adam Larson/Caustic Logic
The Frustrating Fraud, January 23 2007
Although most Pentagon workers in the area hit on 9/11 were still sitting at their desks doing their usual work as Flight 77 came crashing through their office doors, there were well-established and practiced procedures for “exactly” such an event. The Washington Post reported shortly after 9/11 the account of a Pentagon medic who was sitting and reading the just-printed emergency response manual for what to do in case the building was struck by a civilian airliner at the precise moment that happened.  But unfortunately these procedures don’t seem to have helped much, given no radar track of the incoming plane, no warning, and thus no time given to implement any such measures.
Whether the MASCAL crash was supposed to be an accident or an attack didn't seem to matter - it was all about the aftermath. But in the next noteworthy drill conducted eight months later, the preparations were getting more specifically 9/11-related. As US Medicine magazine, "the voice of Federal medicine," reported in October 2001:
"Though the Department of Defense had no capability in place to protect the Pentagon from an ersatz guided missile in the form of a hijacked 757 airliner, DoD medical personnel trained for exactly that scenario in May. In fact, the tri-Service DiLorenzo Health Care Clinic and the Air Force Flight Medicine Clinic here in the Pentagon trained jointly in May to fine-tune their emergency preparedness, afterward making simple equipment changes that would make a difference Sept. 11 when the hypothetical became reality." 
This is amazing; according to this article, they were looking at a hijacked 757 strike four months before that happened on 9/11, preparations that "made a difference." Of course the best difference would have been to simply evacuate the building well before the plane arrived (35 minutes after it became clear the nation was under attack), or to have worked out air defense plans, perhaps with NORAD, to stop any such weaponized aircraft short of the building.
A possible third drill may have been planned to that end in conjunction with a proposed mid-2001 NORAD exercise simulating suicide hijacking attacks. USA Today famously reported on April 18, 2004 that "in the two years before the Sept. 11 attacks, [NORAD] conducted exercises simulating what the White House says was unimaginable at the time: hijacked airliners used as weapons to crash into targets and cause mass casualties." While nearly all of these focused on threats coming from across the Atlantic, they had the 9/11 targets in mind. earlier drills had focused on such an attack against the WTC, in this case “the target was the Pentagon – but that drill was not run after defense officials said it was unrealistic.”  The original source for this is an e-mail from a former NORAD official obtained by the Project On Government Oversight, which explained that NORAD "wanted to develop a response in the event that a terrorist group would use an airliner as a missile to attack the Pentagon, but the Joint Chiefs of Staff rejected the scenario as "too unrealistic."  This was in April 2001 POGO reports, a month before they prepared for defense against an unobstructed hijacked plane/missile hitting their building, and five months before 9/11, when they had no capabilities in place "to protect the Pentagon," but at least they had the aftermath covered well enough.
Buth even with just the two drills plus whatever else went in to the process, the Pentagon's bureaucracy had just enough time to get the emergency procedures ironed out and printed before the precise "unrealistic" scenario envisioned four months earlier came crushingly true. But there was apparently not enough time to fully integrate the plan with things like useful warning procedures - a tragically stalled process that would help illustrate Rumsfeld's charges that pre-9/11, the Pentagon was "tangled in its own anchor chain." How conveniently illustrative of his and his colleagues' known desire for a 21st Century "process of transformation" there.
 Oil Empire. http://www.oilempire.us/wargames.html
 Ryan, Dennis. "Contingency planning Pentagon MASCAL exercise simulates scenarios in preparing for emergencies." Military District of Washington News Service. November 3 2000. Accessed at: http://www.ratical.org/ratville/CAH/linkscopy/ContPlan.html
 Mientka, Matt. Pentagon Medics Trained For Strike. US Medicine. October 2001. http://www.usmedicine.com/article.cfm?articleID=272&issueID=31
 as passed on by US Rep. Jan Schakowski: http://www.house.gov/schakowsky/press2004a/pr4_20_2004mis.html
Also at 9-11 Research: http://911research.wtc7.net/cache/post911/commission/usatoday_noradx.htm
and the original still up at USA Today: http://www.usatoday.com/news/washington/2004-04-18-norad_x.htm
 Project on Government Oversight. "Joint Chiefs of Staff Rejected "Airplanes as Missiles" Scenario Five Months prior to 9/11." April 13 2004. http://www.pogo.org/p/homeland/ha-040401-homelandsecurity.html