In the United States on September 11, 2001 (9/11), 19 terrorists from al-Qaeda hijacked four airplanes in an attempt to crash them into American landmarks. American Airlines Flight 11 and United Airlines Flight 175 crashed into the World Trade Center, and American Airlines Flight 77 was crashed into the Pentagon. United Airlines Flight 93 was intended to be crashed into the U.S. Capitol or White House, but the hijackers intentionally crashed it into a field in Pennsylvania instead, due to a passenger revolt.

Initially, al-Qaeda official Khalid Sheikh Mohammed planned to bomb multiple airliners departing Asia for the U.S. in 1995; the plot was foiled by Manila police before it was enacted. In 1996, he redesigned the plan, wanting nine U.S. airliners to be crashed into U.S. landmarks; al-Qaeda's leader, Osama bin Laden, rejected the plan over its complexity. In 1999, the pair and Mohammed Atef reworked it into what was ultimately carried out on 9/11.

Al-Qaeda then came into contact with the Hamburg cell, a terrorist cell in Germany led by Mohamed Atta. Some of the cell's members then visited camps in Afghanistan where al-Qaeda told them the plan, before the cell regrouped in Germany to work on it. Three of the members eventually piloted the hijacked planes on 9/11: Atta (Flight 11), Marwan al-Shehhi (175), and Ziad Jarrah (93). Flight 77's hijacker-pilot Hani Hanjour was not involved.

At least 19 men chosen by al-Qaeda entered the U.S. in 2000 and 2001. In addition, a potential 20th hijacker named Zacarias Moussaoui was arrested in Minnesota in August 2001. The 19 others split into four groups, and got tickets for four commercial flights on 9/11. During the hijackings, certain members of the groups attacked their respective flights' aircrews, likely using box cutters and mace, which let the others enter the planes' cockpits.

2,977 victims, plus all of the hijackers, died in the attacks. Many of the remaining conspirators in al-Qaeda were captured, then tortured during U.S. interrogations at CIA black sites or the Guantanamo Bay detention camp. Multiple federal investigations were made into 9/11, such as PENTTBOM and the 9/11 Commission. Investigators are split on if Saudi Arabia financed the attacks.

In the Soviet–Afghan War (1979–1989), Muslim-majority Afghanistan was invaded by the mostly non-Muslim Soviet Union. Osama bin Laden, a Saudi Islamist connected to the royal House of Saud, left his country to organize the Afghan mujahideen, Muslims who fought the Soviets as jihadists; those who engage in jihad, Islamic religious struggle, are called mujahideen. For that purpose, bin Laden and Abdullah Yusuf Azzam founded Maktab al-Khidamat (MaK). After the Soviets withdrew from Afghanistan in 1989, Azzam was assassinated in Pakistan. Bin Laden then took full control of MaK, which was absorbed into his organization al-Qaeda.

Due to bin Laden's beliefs, in 1991, the royals exiled him from Saudi Arabia. He moved to Sudan, where he may have had al-Qaeda get involved in the 1993 assault on U.S. troops in Somalia. In 1996, under Saudi and American pressure, Sudan exiled him from their country. Bin Laden returned to Afghanistan, which, by then, was run by the Taliban. They allowed al-Qaeda to use the country as its base of operations.

In 1996, bin Laden issued a fatwa calling for the American troops stationed in Saudi Arabia to leave. He issued another in 1998, calling for all Muslims to take up arms against Americans. He stated that, in choosing targets of their terrorist acts, the organization would not differentiate between civilians and soldiers: "As far as we are concerned, Americans are all targets."