The other 9/11 investigation: ANALYSIS

"We have some planes" was the message broadcast over the FAA aircraft radio system and overheard by Boston Center air traffic control the morning of Sept. 11, 2001.

In short order, four U.S.-flagged aircraft were highjacked.

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

The target of United 93 has long been speculated to have been other than the Pentagon: the U.S. Capitol, perhaps, or the White House, and most likely then-President George W. Bush. However, it wasn't the first time that Osama bin Laden, the late al-Qaida leader who orchestrated the 9/11 attacks, wanted to kill the U.S. president.

In 1996, bin Laden hatched a plot to kill former President Clinton in Manila, only to be foiled by Filipino security officers who recovered a powerful bomb on a bridge that Clinton's motorcade would have taken, as well as an SUV abandoned nearby that contained AK-47assault rifles. They were aided by the quick response of the U.S. Secret Service, which diverted the motorcade upon receiving the threat intelligence.

Bin Laden's preoccupation with assassinating the U.S. president didn't end there. Just weeks after the Sept. 11, 2001 attacks, Egyptian President Hosni Mubarak, as well as Italian government officials, revealed that they'd received intelligence reports that bin Laden's terrorist network was plotting to assassinate President George W. Bush at the G8 summit the previous July in Genoa, Italy, possibly using an aircraft laden with explosives. The reports prompted Italian officials to close the airspace over Genoa and install antiaircraft missiles at the airport.

That threat continued on 9/11 as the attacks were underway. At 9:34 a.m. ET, just three minutes before American Airlines Flight 77 crashed into the Pentagon, Ronald Reagan Washington National Airport advised the Secret Service of an unknown aircraft heading in the direction of the White House. The Secret Service subsequently directed the president and much of Washington, D.C. to evacuate due to 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 mobilized to protect the White House, the vice president, and President Bush, who was being flown around the nation out of concern that a unknown aircraft was potentially targeting Air Force One.

The official 9/11 Commission Report, released in July 2004, said that their investigation revealed that 9/11 attack architect Khalid Sheihk Mohammed's (KSM) "original concept of using one of the hijacked planes to make a media statement was scrapped, but Bin Ladin considered the basic idea feasible." The report further stated that bin Laden, Mohammed, and bin Laden 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 in March 2003 and interrogated by American operatives, "bin Ladin wanted to destroy the White House and the Pentagon, KSM wanted to strike the World Trade Center, and all of them wanted to hit the Capitol," further supporting the idea that bin Laden's main focus was killing the U.S. president.

Presidential protection is under the is sole jurisdiction of the U.S. Secret Service, which is also tasked with protecting many other U.S. government officials. It also has primary jurisdiction in any case that threatens the president, resulting in a full investigation against anyone making that threat, as was the case with Osama bin Laden.

Due to the international implications, the Secret Service opened a case, working it jointly with the FBI and CIA out of the interagency Joint Terrorism Task Force (JTTF). The relatively unknown and top secret presidential threat investigation was so sensitive that to date, it's never been publicly acknowledged – most such threat case investigations never are – but those who were involved have acknowledged that the investigation occurred. While the FBI and Justice Department continued to work on indicting bin Laden and al-Qaida for the multiple attacks against U.S. interests and personnel, protecting the president from assassination remained a priority of the Secret Service and other federal agencies.

"Osama bin Laden boldly commanded his network to organize special cells in Afghanistan and Pakistan to attack the aircraft of President Obama and Gen. David H. Petraeus," the Washington Post reported in 2012, citing documents seized in 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 top lieutenant by saying that President Obama was "the head of infidelity and killing him automatically will make [Vice President] Biden take over the presidency. … Biden is totally unprepared for that post, which will lead the U.S. into a crisis. As for Petraeus, he is the man of the hour … and killing him would alter the war's path" in Afghanistan.

The FBI opened their now famous 9/11 Pentagon/Twin Towers Bombing Investigation (PENTTBOMB) on the day of the 9/11 attacks, the largest investigation in the bureau's history. It tells us with certainty that the World Trade Center and the Pentagon weren't al-Qaida's only targets on Sept. 11, 2001 – and had the passengers onboard United Flight 93 not acted as they did, sacrificing their lives in the process, that flight might instead have crashed into the White House and killed the president, had he been there, or the vice president, who was there.

The 9/11 attacks sent the entire federal law enforcement community into overdrive to try to identify and stop any active threats against nation, and specifically the president. It was an investigation that took them around the world, from Kabul to Baghdad to Guantanamo Bay. Yet even as that global search was underway, Osama bin Laden's desire and determination to assassinate the U.S. president remained.

Richard F. Frankel is an ABC News contributor and former special agent in charge for the FBI. Donald J. Mihalek is an ABC News contributor, retired senior Secret Service agent and regional field training instructor who served on the president's detail and presidential transitions. The opinions expressed in this story are theirs and not those of ABC News.