The origins of al-Qaeda can be traced to 1979 when the Soviet Union invaded Afghanistan.

Osama bin Laden traveled to Afghanistan and helped organize Arab mujahideen to resist the Soviets. Under the guidance of Ayman al-Zawahiri, bin Laden became more radical. In 1996, bin Laden issued his first fatwā, calling for American soldiers to leave Saudi Arabia.

The attacks were conceived by Khalid Sheikh Mohammed, who first presented it to Osama bin Laden in 1996.

In a second fatwā in 1998, bin Laden outlined his objections to American foreign policy with respect to Israel, as well as the continued presence of American troops in Saudi Arabia after the Gulf War. Bin Laden used Islamic texts to exhort Muslims to attack Americans until the stated grievances were reversed. Muslim legal scholars "have throughout Islamic history unanimously agreed that the jihad is an individual duty if the enemy destroys the Muslim countries", according to bin Laden.

In a December 1999 interview, bin Laden said he felt that Americans were "too near to Mecca", and considered this a provocation to the entire Muslim world. One analysis of suicide terrorism suggested that without U.S. troops in Saudi Arabia, al-Qaeda likely would not have been able to get people to commit to suicide missions.

In early 1999, bin Laden gave approval for Mohammed to go forward with organizing the plot. Mohammed, bin Laden, and bin Laden's deputy Mohammed Atef held a series of meetings in early 1999. Atef provided operational support, including target selections and helping arrange travel for the hijackers. Bin Laden overruled Mohammed, rejecting potential targets such as the U.S. Bank Tower in Los Angeles for lack of time.

Bin Laden provided leadership and financial support, and was involved in selecting participants. He initially selected Nawaf al-Hazmi and Khalid al-Mihdhar, both experienced jihadists who had fought in Bosnia.

In late 1999, a group of men from Hamburg, Germany arrived in Afghanistan; the group included Mohamed Atta, Marwan al-Shehhi, Ziad Jarrah, and Ramzi bin al-Shibh. Bin Laden selected these men because they were educated, could speak English, and had experience living in the West. New recruits were routinely screened for special skills and al-Qaeda leaders consequently discovered that Hani Hanjour already had a commercial pilot's license. Mohammed later said that he helped the hijackers blend in by teaching them how to order food in restaurants and dress in Western clothing.

Hazmi and Mihdhar arrived in the United States in mid-January 2000. In early 2000, Hazmi and Mihdhar took flying lessons in San Diego, California, but both spoke little English, performed poorly in flying lessons, and eventually served as secondary – or "muscle" – hijackers.

Hanjour arrived in San Diego on December 8, 2000, joining Hazmi. They soon left for Arizona, where Hanjour took refresher training.

On May 1, 2001, the CIA informed the White House that "a group presently in the United States" was in the process of planning a terrorist attack.

The President's Daily Brief on June 29, 2001, stated that "[the United States] is not the target of a disinformation campaign by Osama Bin Laden". The document repeated evidence surrounding the threat, "including an interview that month with a Middle Eastern journalist in which Bin Laden aides warned of a coming attack, as well as competitive pressures that the terrorist leader was feeling, given the number of Islamists being recruited for the separatist Russian region of Chechnya." The CIA reiterated that the attacks were anticipated to be near-term and have "dramatic consequences".

In July 2001, J. Cofer Black, CIA's couterterrorism chief and George Tenet, CIA's director, met with Condoleezza Rice, the National Security Advisor, to inform her about communications intercepts and other top-secret intelligence showing the increasing likelihood that al-Qaeda would soon attack the United States. Rice listened but was unconvinced, having other priorities on which to focus. Secretary of Defense Donald Rumsfeld questioned the information suggesting it was a deception meant to gauge the U.S. response.

In July 2001, Atta met with bin al-Shibh in Spain, where they coordinated details of the plot, including final target selection. Bin al-Shibh also passed along bin Laden's wish for the attacks to be carried out as soon as possible. Some of the hijackers received passports from corrupt Saudi officials who were family members, or used fraudulent passports to gain entry.

On August 6, 2001, the President's Daily Briefing, entitled Bin Ladin Determined to Strike in US warned that bin Laden was planning to exploit his operatives' access to the U.S. to mount a terrorist strike: FBI information... indicates patterns of suspicious activity in this country, consistent with preparations for hijackings or other types of attack. Rice responded to the claims about the briefing in a statement before the 9/11 Commission stating the brief was "not prompted by any specific threat information" and "did not raise the possibility that terrorists might use airplanes as missiles."

In mid-August, one Minnesota flight school alerted the FBI about Zacarias Moussaoui, who had asked "suspicious questions." The FBI found that Moussaoui was a radical who had traveled to Pakistan, and the INS arrested him for overstaying his French visa. Their request to search his laptop was denied by FBI headquarters due to the lack of probable cause.

American Airlines Flight 11: a Boeing 767 aircraft, departed Logan Airport at 7:59 a.m. en route to Los Angeles with a crew of 11 and 76 passengers, not including five hijackers. The hijackers flew the plane into the northern facade of the North Tower of the World Trade Center in New York City at 8:46 a.m. Mohamed Atta deliberately crashed the plane into the North Tower of the World Trade Center in New York City, killing all 92 people aboard and an unknown number in the building's impact zone. The aircraft involved, a Boeing 767-223ER, registration N334AA.

United Airlines Flight 175: a Boeing 767 aircraft, departed Logan Airport at 8:14 a.m. en route to Los Angeles with a crew of nine and 51 passengers, not including five hijackers. The hijackers flew the plane into the southern facade of the South Tower of the World Trade Center in New York City at 9:03 a.m. Approximately thirty minutes into the flight, the hijackers forcibly breached the cockpit and overpowered the pilot and first officer, allowing lead hijacker and trained pilot Marwan al-Shehhi to take over the controls.

At 8:32 a.m. FAA officials were notified Flight 11 had been hijacked and they, in turn, notified the North American Aerospace Defense Command (NORAD). (before collision)

United Airlines Flight 93: a Boeing 757 aircraft, departed Newark International Airport at 8:42 a.m. en route to San Francisco, with a crew of seven and 33 passengers, not including four hijackers. As passengers attempted to subdue the hijackers, the aircraft crashed into a field in Stonycreek Township near Shanksville, Pennsylvania, at 10:03 a.m. Ziad Jarrah, who had trained as a pilot, took control of the aircraft and diverted it back toward the east coast, in the direction of Washington, D.C., the U.S. capital. Khalid Sheikh Mohammed and Ramzi bin al-Shibh, considered principal instigators of the attacks, have claimed that the intended target was the U.S. Capitol Building.

At 8:46 a.m., five hijackers crashed American Airlines Flight 11 into the northern façade of the World Trade Center's North Tower (1 WTC).

NORAD scrambled two F-15s from Otis Air National Guard Base in Massachusetts and they were airborne by 8:53 a.m. Because of slow and confused communication from FAA officials, NORAD had 9 minutes notice that Flight 11 had been hijacked, and no notice about any of the other flights before they crashed. (after the first collision (American Airlines Flight 11)).

At 9:03 a.m., another five hijackers crashed United Airlines Flight 175 into the southern façade of the South Tower (2 WTC). The death toll from this collision is 2,606 in the World Trade Center and in the surrounding area.

American Airlines Flight 77: a Boeing 757 aircraft, departed Washington Dulles International Airport at 8:20 a.m. en route to Los Angeles with a crew of six and 53 passengers, not including five hijackers. The hijackers flew the plane into the western facade of the Pentagon in Arlington County, Virginia, at 9:37 a.m. Hani Hanjour, one of the hijackers who was trained as a pilot, assumed control of the flight. Unknown to the hijackers, passengers aboard made telephone calls to friends and family and relayed information on the hijacking.

After both of the Twin Towers had already been hit, more fighters were scrambled from Langley Air Force Base in Virginia at 9:30 a.m.

Five hijackers flew American Airlines Flight 77 into the Pentagon at 9:37 a.m. The death toll from this collision is 125.

At 9:42 a.m., the Federal Aviation Administration (FAA) grounded all civilian aircraft within the continental U.S., and civilian aircraft already in flight were told to land immediately. All international civilian aircraft were either turned back or redirected to airports in Canada or Mexico, and were banned from landing on United States territory for three days.

Three buildings in the World Trade Center collapsed due to fire-induced structural failure. The South Tower collapsed at 9:59 a.m. after burning for 56 minutes in a fire caused by the impact of United Airlines Flight 175 and the explosion of its fuel.

At 10:20 a.m. Vice President Dick Cheney issued orders to shoot down any commercial aircraft that could be positively identified as being hijacked. These instructions were not relayed in time for the fighters to take action.

The North Tower collapsed at 10:28 a.m. after burning for 102 minutes.

A fourth flight, United Airlines Flight 93, crashed near Shanksville, Pennsylvania, southeast of Pittsburgh, at 10:03 a.m. after the passengers fought the four hijackers. Flight 93's target is believed to have been either the Capitol or the White House.

At 2:40 p.m. in the afternoon of September 11, Secretary of Defense Donald Rumsfeld was issuing rapid orders to his aides to look for evidence of Iraqi involvement. According to notes taken by senior policy official Stephen Cambone, Rumsfeld asked for, "Best info fast. Judge whether good enough hit S.H. [Saddam Hussein] at same time. Not only UBL" [Osama bin Laden].

When the North Tower collapsed, debris fell on the nearby 7 World Trade Center building (7 WTC), damaging it and starting fires. These fires burned for hours, compromising the building's structural integrity, and 7 WTC collapsed at 5:21 p.m.

The attacks caused the deaths of 2,996 people (including all 19 hijackers) and injured more than 6,000 others. The death toll included 265 on the four planes (from which there were no survivors). Most of those who perished were civilians, with the exception of 343 firefighters, 72 law enforcement officers, 55 military personnel, and the 19 terrorists who died in the attacks.

Early on the morning of September 11, 2001, 19 hijackers took control of four commercial airliners (two Boeing 757s and two Boeing 767s) en route to California (three headed to LAX in Los Angeles and one to SFO in San Francisco).

Two dozen members of Osama bin Laden's family were urgently evacuated out of the country on a private charter plane under FBI supervision three days after the attacks.

On September 14, 2001, the U.S. Congress passed the Authorization for Use of Military Force Against Terrorists. Still in effect, it grants the President the authority to use all "necessary and appropriate force" against those whom he determined "planned, authorized, committed or aided" the September 11 attacks, or who harbored said persons or groups.

There were reports of attacks on mosques and other religious buildings (including the firebombing of a Hindu temple), and assaults on people, including one murder: Balbir Singh Sodhi, a Sikh mistaken for a Muslim, was fatally shot on September 15, 2001, in Mesa, Arizona.

Bin Laden orchestrated the attacks and initially denied involvement but later recanted his false statements. Al Jazeera broadcast a statement by bin Laden on September 16, 2001, stating, "I stress that I have not carried out this act, which appears to have been carried out by individuals with their own motivation."

In the aftermath of the attacks, tens of thousands of people attempted to flee Afghanistan due to the possibility of a military retaliation by the United States. Pakistan, already home to many Afghan refugees from previous conflicts, closed its border with Afghanistan on September 17, 2001.

Shortly after the attacks, President Bush made a public appearance at Washington, D.C.'s largest Islamic Center and acknowledged the "incredibly valuable contribution" that millions of American Muslims made to their country and called for them "to be treated with respect.".

On September 20, 2001, President George W. Bush addressed the nation and a joint session of the United States Congress regarding the events of September 11 and the subsequent nine days of rescue and recovery efforts, and described his intended response to the attacks. New York City mayor Rudy Giuliani's highly visible role won him high praise in New York and nationally.

On September 25, 2001, Iran's fifth president, Mohammad Khatami meeting British Foreign Secretary, Jack Straw, said: "Iran fully understands the feelings of the Americans about the terrorist attacks in New York and Washington on September 11." He said although the American administrations had been at best indifferent about terrorist operations in Iran (since 1979), the Iranians instead felt differently and had expressed their sympathetic feelings with bereaved Americans in the tragic incidents in the two cities. He also stated that "Nations should not be punished in place of terrorists."

On September 27, 2001, FBI released photos of all 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 from Egypt, and one from Lebanon.

The aftermath of the 9/11 attack resulted in immediate responses to the event, including domestic reactions, hate crimes, Muslim American responses to the event, international responses to the attack, and military responses to the events. An extensive compensation program was quickly established by Congress in the aftermath to compensate the victims and families of victims of the 9/11 attack as well.

On October 7, 2001, the War in Afghanistan began when U.S. and British forces initiated aerial bombing campaigns targeting Taliban and al-Qaeda camps, then later invaded Afghanistan with ground troops of the Special Forces.

In November 2001, U.S. forces recovered a videotape from a destroyed house in Jalalabad, Afghanistan. In the video, bin Laden is seen talking to Khaled al-Harbi and admits foreknowledge of the attacks.

This eventually led to the overthrow of the Taliban rule of Afghanistan with the Fall of Kandahar on December 7, 2001, by U.S.-led coalition forces. Conflict in Afghanistan between the Taliban insurgency and the Afghan forces backed by NATO Resolute Support Mission is ongoing.

The last fires at the World Trade Center site were extinguished on December 20, exactly 100 days after the attacks.

On December 27, 2001, a second bin Laden video was released. In the video, bin Laden said: It has become clear that the West in general and America in particular have an unspeakable hatred for Islam. ... It is the hatred of crusaders. Terrorism against America deserves to be praised because it was a response to injustice, aimed at forcing America to stop its support for Israel, which kills our people. ... We say that the end of the United States is imminent, whether Bin Laden or his followers are alive or dead, for the awakening of the Muslim umma (nation) has occurred.

In spring of 2001, the secondary hijackers began arriving in the United States.

In 2001 dollars, U.S. stocks lost $1.4 trillion in valuation for the week.

Journalist Yosri Fouda of the Arabic television channel Al Jazeera reported that in April 2002, Khalid Sheikh Mohammed admitted his involvement in the attacks, along with Ramzi bin al-Shibh.

After months of around-the-clock operations, the World Trade Center site was cleared by the end of May 2002.

The National Commission on Terrorist Attacks Upon the United States (9/11 Commission), chaired by Thomas Kean and Lee H. Hamilton, 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.

The damaged section of the Pentagon was rebuilt and occupied within a year of the attacks.

Exposure to the toxins in the debris is alleged to have contributed to fatal or debilitating illnesses among people who were at Ground Zero. The Bush administration ordered the Environmental Protection Agency (EPA) to issue reassuring statements regarding air quality in the aftermath of the attacks, citing national security, but the EPA did not determine that air quality had returned to pre-September 11 levels until June 2002.

Khalid Sheikh Mohammed was arrested on March 1, 2003, in Rawalpindi, Pakistan, by Pakistani security officials working with the CIA. He was then held at multiple CIA secret prisons and Guantanamo Bay where he was interrogated and tortured with methods including waterboarding.

By the deadline for victim's compensation on September 11, 2003, 2,833 applications had been received from the families of those who were killed.

The failures in intelligence-sharing were attributed to 1995 Justice Department policies limiting intelligence sharing, combined with CIA and NSA reluctance to reveal "sensitive sources and methods" such as tapped phones. Testifying before the 9/11 Commission in April 2004, then-Attorney General John Ashcroft recalled that the "single greatest structural cause for the September 11th problem was the wall that segregated or separated criminal investigators and intelligence agents."

On July 22, 2004, the Commission issued the 9/11 Commission Report. The report detailed the events of 9/11, found 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, "We believe the 9/11 attacks revealed four kinds of failures: in imagination, policy, capabilities, and management".

In 2004, Bin Laden claimed that the idea of destroying the towers had first occurred to him in 1982, when he witnessed Israel's bombardment of high-rise apartment buildings during the 1982 Lebanon War. Some analysts, including Mearsheimer and Walt, also claimed that U.S. support of Israel was one motive for the attacks.

The 2004 9/11 Commission Report determined that the animosity towards the United States felt by Mohammed, the principal architect of the 9/11 attacks, stemmed from his "violent disagreement with U.S. foreign policy favoring Israel".

On September 26, 2005, the Spanish high court sentenced Abu Dahdah to 27 years in prison for conspiracy on the 9/11 attacks and being a member of the terrorist organization al-Qaeda. At the same time, another 17 al-Qaeda members were sentenced to penalties of between six and eleven years.

The construction of One World Trade Center began on April 27, 2006, and reached its full height on May 20, 2013. The spire was installed atop the building at that date, putting 1 WTC's height at 1,776 feet (541 m) and thus claiming the title of the tallest building in the Western Hemisphere.

One of the first memorials was the Tribute in Light, an installation of 88 searchlights at the footprints of the World Trade Center towers. In New York City, the World Trade Center Site Memorial Competition was held to design an appropriate memorial on the site. The winning design, Reflecting Absence, was selected in August 2006, and consists of a pair of reflecting pools in the footprints of the towers, surrounded by a list of the victims' names in an underground memorial space.

Another video obtained by Al Jazeera in September 2006 shows bin Laden with Ramzi bin al-Shibh, as well as two hijackers, Hamza al-Ghamdi and Wail al-Shehri, as they make preparations for the attacks.

Bone fragments were still being found in 2006 by workers who were preparing to demolish the damaged Deutsche Bank Building.

During U.S. hearings at Guantanamo Bay in March 2007, Mohammed again confessed his responsibility for the attacks, stating he "was responsible for the 9/11 operation from A to Z" and that his statement was not made under duress.

In May 2007, senators from both major 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".

In Arlington County, the Pentagon Memorial was completed and opened to the public on the seventh anniversary of the attacks in 2008. It consists of a landscaped park with 184 benches facing the Pentagon. When the Pentagon was repaired in 2001–2002, a private chapel and indoor memorial were included, located at the spot where Flight 77 crashed into the building.

On December 22, 2010, the United States Congress passed the James L. Zadroga 9/11 Health and Compensation Act. It allocated $4.2 billion to create the World Trade Center Health Program, which provides testing and treatment for people suffering from long-term health problems related to the 9/11 attacks.

In 2010, a team of anthropologists and archaeologists searched for human remains and personal items at the Fresh Kills Landfill, where 72 more human remains were recovered, bringing the total found to 1,845. DNA profiling continues in an attempt to identify additional victims.

After a 10-year manhunt, U.S. President Barack Obama announced that bin Laden was killed by American special forces in his compound in Abbottabad, Pakistan, on May 1, 2011.

The memorial was completed on September 11, 2011.

The Borough of Manhattan Community College's Fiterman Hall at 30 West Broadway was condemned due to extensive damage in the attacks, and was reopened in 2012.

On the World Trade Center site, three more office towers were to be built one block east of where the original towers stood. 4 WTC, meanwhile, opened in November 2013, making it the second tower on the site to open behind 7 World Trade Center, as well as the first building on the Port Authority property.

A museum also opened on site on May 21, 2014.

In Shanksville, a concrete and glass visitor center was opened on September 10, 2015, situated on a hill overlooking the crash site and the white marble Wall of Names. An observation platform at the visitor center and the white marble wall are both aligned beneath the path of Flight 93.

The PATH train system's World Trade Center station was located under the complex. As a result, the entire station was demolished completely when the towers collapsed, and the tunnels leading to Exchange Place station in Jersey City, New Jersey were flooded with water. The station was rebuilt as the $4 billion World Trade Center Transportation Hub, which reopened in March 2015.

In July 2016, the Obama administration released a document, compiled by US investigators Dana Lesemann and Michael Jacobson, known as "File 17", which contains a list naming three dozen people, including the suspected Saudi intelligence officers attached to Saudi Arabia's embassy in Washington, D.C., which connects Saudi Arabia to the hijackers.

3 WTC opened on June 11, 2018, becoming the fourth skyscraper at the site to be completed.

The Cortlandt Street station on the New York City Subway's IRT Broadway–Seventh Avenue Line was also in close proximity to the World Trade Center complex, and the entire station, along with the surrounding track, was reduced to rubble. The latter station was rebuilt and reopened to the public on September 8, 2018.

A letter presented by the lawyers of Khaled Sheikh Mohammed in the U.S. District Court, Manhattan on 26 July 2019 indicated that he was interested in testifying about Saudi Arabia’s role in the 9/11 attacks and helping the victims and families of the victims of 9/11 in exchange for the United States not seeking the death penalty against him. James Kreindler, one of the lawyers for the victims, raised question over the usefulness of Mohammed.