Even without phase two or its predecessor report, Al Qaeda’s and others’ shift to suicide hijackings was not a theoretical – it actually happened and manifested itself in the real world. Numerous reminders of the tactic had popped up since 1995 in the form of foiled attempts, intercepted plots, and ominous warnings from various quarters. In November 1996, for example, Ethiopian terrorists hijacked an airliner and tried to crash it into a beach resort in the Comoros Islands for unclear reasons. Reports from the time explained that the pilots were able though to dive the plane into the sea, saving the resort by a bare 500 yards, but killing all but 52 of the 175 souls on board. 
Suicide hijacking was a fear at both the 1996 and 2000 Olympics (in Atlanta, GA and Sydney, Australia, respectively). In the 1996 case, Richard Clarke personally toured Atlanta looking for security breaches. He was horrified. Among his concerns was air security; ”mindful of Ramzi Yousef’s plot to blow up 747s and the images of Pan Am 103, I asked about aircraft. “What if somebody blows up a 747 over the Olympic Stadium. Or even flies one into the stadium?””  Clarke could see in 1996 someone hijacking an airliner and crashing it into the stadium, and he was thinking Bojinka. In fact, this was not just a thought in Clarke’s head – security for the ’96 Olympics was actually beefed-up to meet the threat. The Chicago Tribune reported in November 2001:
”In an extraordinary aerial dragnet, launched quietly that summer and kept largely under wraps ever since, Black Hawk helicopters and U.S. Customs Service jets were deployed to intercept suspicious aircraft in the skies over the Olympic venues [...] Agents monitored crop duster flights within hundreds of miles […] Law-enforcement agents also fanned out to regional airports throughout northern Georgia "to make sure nobody hijacked a small aircraft and tried to attack one of the venues," said Woody Johnson, the FBI agent in charge of the Atlanta office at the time.”
A handful of government-commissioned reports highlighted the threat of aircraft as weapons in the hands of terrorists, or at least tried to. One was a September 1999 report called “Sociology and Psychology of Terrorism: Who Becomes a Terrorist and Why?” It was prepared for the CIA-connected National Intelligence Council and shared with other federal agencies. CBS News cited it in May 2002: “Suicide bomber(s) belonging to al Qaeda's Martyrdom Battalion could crash-land an aircraft packed with high explosives into the Pentagon, the headquarters of the CIA, or the White House.” Author Rex Hudson explained at the time “Ramzi Yousef had planned to do this against the CIA headquarters.”  This is one of the very few pre-9-11 admissions of phase two that I’ve seen.
The Bojinka fears that should have been closest on president Bush’s mind on the morning of 9-11 had come less than two months earlier, in Late July. As reported in the Los Angeles Times, Italian authorities felt that there was a serious possibility of an attack against Bush and other world leaders attending the G8 Summit in Genoa by “crashing an airliner” into the venue. The threat was considered unsubstantiated by U.S. officials, but Italian authorities closed the airspace over Genoa and placed antiaircraft guns around the summit complex to enforce the order. For added security, the Secret Service had Bush sleep every night on an aircraft carrier just off the coast.  He had to have been told why he was drifting in the steel belly of that big boat instead of lying on fine linens in a posh Genoese resort.
 Thompson, Paul and the center for Cooperative Research. “The Terror Timeline.” 2004. Page 18.
 Clarke, Richard. “Against All Enemies.” Page 106.
 Fineman, Mark and Judy Pasternak. “'96 Games warned of air threat.” Chicago Tribune. November 18, 2001http://www.chicagotribune.com/search/chi-0111180092nov18.story
 “'99 Report Warned Of Suicide Hijacking.” CBS News. May 17, 2002.
 “Italy Tells of Threat at Genoa Summit” LA Times. September 27, 2001. http://www.latimes.com/news/nationworld/nation/la-092701genoa.story