Much of the information I’ve drawn on so far in analyzing Bojinka is from an excellent article on the plot published in December 2001. It was by Matthew Brzezinski, ordinarily a writer of fiction known for his 2001 novel Casino Moscow: A Tale of Greed and Adventure on Capitalism's Wildest Frontier, which was praised by Foreign Affairs magazine as “a shake-your-head, laugh-out-loud book, but one with a good deal to say.”  Yet he has also written one of the most widely read factual accounts of Bojinka’s discovery, originally published as “Bust and Boom” in the Washington Post magazine, and published elsewhere as “Operation Bojinka’s Bombshell.” In the article, Brzezinski noted “the suicide attacks coincided, almost to the day, with another fifth anniversary: the 1996 conviction, in a Manhattan court, of Bojinka's original plotters.”  September 11 is hardly close enough to the 5th to constitute much of an anniversary, but it does help Brzezinski close his article on an ominous note that ties this fantastic plot yet closer to the far more fantastic 2001 attacks. He also took a hard line in the new “War on Terror.” He said of suspects captured in Afghanistan and elsewhere “the last thing we want is having these guys back in circulation.” But he advised patience in taking them out; “we would be better served interrogating the life out of them rather than carrying out any sort of ‘swift justice.’” 
Aida Fariscal, whom Brzezinski describes as “a disgruntled former cop,” and his primary source for the article, was cited by the CIA for her leading role in busting up Bojinka and saving perhaps thousands of lives. After 9/11 she said “this should have never, ever been allowed to happen. All those poor people dead.”  (Does she know of another way to get “useful casualty lists?”) In a Washington Post Q and A session with Brzezinski following release of his story, one question pitched was “how much of the evidence that was documented in the Philippines […] could have been fabricated? I'm not questioning the veracity of your reporting. I'm just wondering if the Philippine government is seeking for a handout to “combat terrorism” when in reality they might use it for other operations.” Brzezinski admitted money was a factor, but noted of Fariscal’s account “I tend to believe its authenticity since her interests and those of the Philippine [government] don't necessarily coincide. Besides U.S. intelligence sources have not disputed any of its validity, even though the material is clearly embarrassing to them.” 
While we might wonder what the Filipinos did with the money they were given (Clinton, the Pope, and eleven airliner bombings, all narrowly averted in one arrest! That’s gotta be worth some Benjamins), one could also wonder what American authorities would get out of the bargain. The embarrassment from Brzezinski’s “bombshell” may have seemed a small price to pay for such a coup of a cover story for Shadow 9-11. And it could’ve been more embarrassing, but Matt had damage control in mind. Despite Bojinka in both its phases, as he had just reported it, he said after his story was published, “no one imagined something like this [was] possible, and there was no US precedent to justify heightened security. Bojinka was about blowing planes up, not hijacking them.” 
As Matthew noted: “Bojinka was about blowing planes up, not hijacking them.” From Matt’s account were missing two key elements that might have made the connection unavoidable. Suicide attack from the air was there, but it was one guy in a small plane – the missing links to become 9/11 would be an increase in scale - hijacking an airliner - and multiplying that into synchronized suicide hijackings.
Peter Lance, a veteran investigative reporter with ABC News, TV writer (Miami Vice, Missing Persons, etc.), and a regular guest on Coast to Coast AM, is a respected expert the massive government “cover-up” over its incompetence and underestimation of al Qaeda.  Lance is not a subscriber to Shadow 9-11 by a long shot, but his analysis of the Bojinka plot is worthy of note. In his book 1,000 Years for Revenge (2003) he explained that Murad’s phase two was from the beginning centered not on crop dusters with bombs but on a suicide hijacking of an airliner. Lance cites as clear evidence a January 20, 1995 memo written by Col. Rodolfo Mendoza, Murad’s main interrogator:
”What the subject [has] in his mind is that he will board any American commercial aircraft pretending to be an ordinary passenger. Then he will hijack said aircraft, control its cockpit, and dive it at the CIA headquarters. He will use no bomb or explosives. It is simply a suicidal mission that he is very much willing to execute.” 
While Brzezinski’s two-phase Bojinka collectively hinted at 9/11, Mendoza’s account is of a plan that Lance accurately calls “a virtual blueprint of the 9/11 attacks,” if one simply multiplies by four - or divides by three. Lance also cites Murad mentioning ten other men receiving flight training at the time of his arrest, indicating that phase two was more ambitious even than what happened, planning eleven suicide hijackings to match the lofty number in the famous phase one.  Murad’s “more trained pilots” were already hitting the books and the simulators at the time of his arrest, and pending the provision of eleven teams of backup “muscle” hijackers, the plan was set. Philippine authorities say they passed all this information on to their U.S. counterparts. 
So why the earlier reports from U.S. and Philippine sources referring to a bomb-laden crop-duster or Cessna at the heart of Murad’s plot (when the plot is mentioned at all)? Was Mendoza’s memo, or the batch of terrorists earning their wings, suppressed from the record for some reason? Why didn’t Brzezinski’s investigation turn up this exaggerated 9-11 script written up in 1994, instead offering a muted, distanced version like a Muslim Frank Corder?