Immediately after the attacks, the Federal Bureau of Investigation started PENTTBOM, the largest criminal inquiry in the history of the United States. At its height, more than half of the FBI's agents worked on the investigation and followed a half-million leads. The FBI concluded that there was "clear and irrefutable" evidence linking al-Qaeda and bin Laden to the attacks. The FBI was able to quickly identify the hijackers, including leader Mohamed Atta, when his luggage was discovered at Boston's Logan Airport. Due to a mix-up, the luggage failed to make it aboard American Airlines Flight 11 as planned. The luggage contained the hijackers' names, assignments and al-Qaeda connections. "It had all these Arab-language papers that amounted to the Rosetta stone of the investigation", said one FBI agent.
Within hours of the attacks, the FBI released the names and in many cases the personal details of the suspected pilots and hijackers. By midday, the U.S. National Security Agency and German intelligence agencies had intercepted communications pointing to Osama bin Laden. On September 27, 2001, the FBI released photos of the 19 hijackers, along with information about possible nationalities and aliases. Fifteen of the men were from Saudi Arabia, two from the United Arab Emirates, one (Atta) from Egypt, and one from Lebanon.
The National Commission on Terrorist Attacks Upon the United States (9/11 Commission), chaired by former New Jersey Governor Thomas Kean, was formed in late 2002 to prepare a thorough account of the circumstances surrounding the attacks, including preparedness for and the immediate response to the attacks. On July 22, 2004, the 9/11 Commission issued the 9/11 Commission Report. The report detailed the events of 9/11, that the attacks were carried out by members of al-Qaeda and examined how security and intelligence agencies were inadequately coordinated to prevent the attacks. Formed from an independent bipartisan group of mostly former Senators, Representatives and Governors, the commissioners explained that, "We believe the 9/11 attacks revealed four kinds of failures: in imagination, policy, capabilities, and management". The commission made numerous recommendations on how to prevent future attacks, and in 2011 were dismayed that more of their recommendations had yet to be implemented.
Collapse of the World Trade Center
The U.S. National Institute of Standards and Technology investigated the collapses of the Twin Towers and 7 WTC. The goals of the investigation were to determine why the buildings collapsed, the extent of injuries and fatalities, and the procedures involved in designing and managing the World Trade Center. The investigation into the collapse of 1 WTC and 2 WTC was concluded in October 2005, and the investigation into the collapse of 7 WTC concluded in August 2008.
The NIST found that the fireproofing on the Twin Towers' steel infrastructures was blown off by the initial impact of the planes and that, had this not occurred, the towers would likely have remained standing. A study published by researchers of Purdue University confirmed that, if the thermal insulation on the core columns were scoured off and column temperatures were elevated to approximately 700 °C (1,292 °F), the fire would have been sufficient to initiate collapse.
W. Gene Corley, director of the original investigation, commented that, "the towers really did amazingly well. The terrorist aircraft didn’t bring the buildings down; it was the fire which followed. It was proven that you could take out two thirds of the columns in a tower and the building would still stand." The fires weakened the trusses supporting the floors, making the floors sag. The sagging floors pulled on the exterior steel columns causing the exterior columns to bow inward. With the damage to the core columns, the buckling exterior columns could no longer support the buildings, causing them to collapse. In addition, the report found the towers' stairwells were not adequately reinforced to provide emergency escape for people above the impact zones. NIST concluded that uncontrolled fires in 7 WTC caused floor beams and girders to heat and subsequently "caused a critical support column to fail, initiating a fire-induced progressive collapse that brought the building down".
Internal review of the CIA
The Inspector General of the CIA conducted an internal review of the CIA's pre-9/11 performance and was harshly critical of senior CIA officials for not doing everything possible to confront terrorism. He criticized their failure to stop two of the 9/11 hijackers, Nawaf al-Hazmi and Khalid al-Mihdhar, as they entered the United States and their failure to share information on the two men with the FBI. In May 2007, senators from both the U.S. political parties drafted legislation to make the review public. One of the backers, Senator Ron Wyden said, "The American people have a right to know what the Central Intelligence Agency was doing in those critical months before 9/11."
On the day of the attacks, New York City mayor Rudy Giuliani proclaimed, "We will rebuild. We're going to come out of this stronger than before, politically stronger, economically stronger. The skyline will be made whole again."
The damaged section of the Pentagon was rebuilt and occupied within a year of the attacks. The temporary World Trade Center PATH station opened in late 2003 and construction of the new 7 World Trade Center was completed in 2006. Work on rebuilding the main World Trade Center site was delayed until late 2006 when leaseholder Larry Silverstein and the Port Authority of New York and New Jersey agreed on financing. 1 World Trade Center is currently under construction at the site and at 1,776 ft (541 m) upon completion in 2014, will become the tallest building in North America.On the World Trade Center site, three more towers were expected to be built one block east of where the original towers stood. Though initial construction has commenced on all three towers, they are expected to be completed slightly after the completion of One World Trade Center.