The other 9/11 investigation: ANALYSIS

“We have some aircraft,” was the message sent over the FAA’s onboard radio system and overheard by air traffic control at Boston Center on the morning of September 11, 2001.

Within a short period of time, four US-flagged aircraft were hijacked.

American Airlines Flight 11 was intentionally flown into the North Tower of the World Trade Center at 8:46 a.m. ET, while United Flight 175 was intentionally flown into the South Tower at 9:03 a.m. American Airlines Flight 77 crashed into the Pentagon 34 minutes later, and United Flight 93 — with passengers on board who bravely fought off their hijackers — crashed in a field outside Shanksville, Pennsylvania, at 10:03 a.m.

The target of United 93 was far from the Pentagon, but perhaps the U.S. Capitol or the White House, and most likely then-President George W. Bush. However, it was not the first time that Osama bin Laden, the late al-Qaeda leader who orchestrated the September 11 attacks, wanted to kill the U.S. president.

In 1996, bin Laden hatched a plan to kill former President Clinton in Manila, but it was thwarted by Philippine security officials who discovered a high-yield bomb on a bridge that Clinton's motorcade would have captured, and a nearby SUV containing AK-47 assault rifles. They were aided by the quick response of U.S. intelligence, which rerouted the motorcade after receiving intelligence about the threat.

Bin Laden's obsession with assassinating the U.S. president did not end there. Just weeks after the September 11, 2001 attacks, Egyptian President Hosni Mubarak and Italian government officials announced that they had received intelligence reports that bin Laden's terrorist network was planning to assassinate President George W. Bush at the G8 summit in Genoa the previous July, possibly using an airplane loaded with explosives. The reports prompted Italian authorities to close the airspace over Genoa and install anti-aircraft missiles at the airport.

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This threat continued on September 11, as the attacks were underway. At 9:34 a.m. Eastern Time, just three minutes before American Airlines Flight 77 crashed into the Pentagon, the Secret Service at Ronald Reagan Washington National Airport was notified of an unidentified aircraft heading toward the White House. The Secret Service then ordered the President and much of Washington, D.C. to evacuate because of the threat. At the White House, Vice President Cheney and his staff were evacuated to the Presidential Emergency Operations Center beneath the White House, known as the “bunker,” while Secret Service agents and officers were mobilized to protect the White House, the Vice President, and President Bush, who was flown across the country for fear that an unidentified aircraft might attack Air Force One.

The official 9/11 Commission report of July 2004 stated that their investigation found that “9/11 attack architect Khalid Sheihk Mohammed (KSM)'s original plan to use one of the hijacked planes for a media statement was scrapped, but bin Laden found the basic idea feasible.” The report further states that bin Laden, Mohammed, and bin Laden's deputy Mohammed Atef “developed an initial list of targets” that included the White House, the U.S. Capitol, the Pentagon, the World Trade Center, and several other targets.

The report also states that according to KSM, who was captured and interrogated by American agents in March 2003, “bin Laden wanted to destroy the White House and the Pentagon, KSM wanted to attack the World Trade Center, and everyone else wanted to hit the Capitol,” further supporting the assumption that bin Laden's main goal was to kill the US president.

The protection of the President is the sole responsibility of the US Secret Service, which is also responsible for the protection of numerous other US government officials. It also has primary responsibility in any case where the President is threatened, leading to a full investigation of anyone who makes that threat, as was the case with Osama bin Laden.

Because of the international implications, the Secret Service opened a case and worked it jointly with the FBI and CIA as part of the interagency Joint Terrorism Task Force (JTTF). The relatively unknown and top-secret investigation into the threat to the president was so sensitive that it was never publicly acknowledged to this day—like most investigations into such threat cases—but those involved have acknowledged that the investigation took place. While the FBI and the Justice Department continued to work to indict bin Laden and al-Qaeda for the numerous attacks on U.S. interests and personnel, protecting the president from assassination attempts remained a priority of the Secret Service and other federal agencies.

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“Osama bin Laden boldly ordered his network to organize special cells in Afghanistan and Pakistan to attack the planes of President Obama and Gen. David H. Petraeus,” the Washington Post reported in 2012, citing documents seized during the raid on bin Laden's compound in Abbottabad, Pakistan, on May 2, 2011, when he was killed by U.S. Navy SEALs. Bin Laden justified his plan to a senior lieutenant by saying that President Obama was “the head of disloyalty and his killing would automatically [Vice President] Biden is taking over as president. … Biden is completely unprepared for this post that will plunge the United States into crisis. As for Petraeus, he is the man of the hour … and killing him would change the course of the war in Afghanistan.”

The FBI opened its now famous Pentagon and Twin Towers Bombing (PENTTBOMB) investigation on the day of the September 11 attacks, the largest investigation in FBI history. It tells us with certainty that the World Trade Center and the Pentagon were not al-Qaeda's only targets on September 11, 2001 – and had the passengers on board United Flight 93 not acted as they did and sacrificed their lives in the process, that flight might have crashed into the White House instead, killing the President, if he had been there, or the Vice President, who was there.

After the September 11 attacks, all federal law enforcement agencies were in overdrive to identify and stop any active threats to the country and especially to the president. The investigation took them all over the world, from Kabul to Baghdad to Guantanamo Bay. But even during this worldwide manhunt, Osama bin Laden's desire and determination to assassinate the US president remained.

Richard F. Frankel is an ABC News contributor and former FBI special agent. Donald J. Mihalek is an ABC News contributor, retired senior intelligence agent and regional field instructor who served on the President's Special Operations Team and during presidential transitions. The opinions expressed in this story are their own and not those of ABC News.

The Other 9/11 Investigation: ANALYSIS originally appeared on abcnews.go.com