Anger followed, as did two wars in far off lands.
Now Mohammed is coming back to the city he allegedly attacked to face a federal civilian jury. He will be tried in a courthouse just blocks from where the towers once stood.
Prosecutors expect to seek the death penalty, Attorney General Eric Holder said at a news conference Friday.
Holder said five other suspects, including a major suspect in the bombing of the USS Cole warship, Abd al-Rahim al-Nashiri, will be tried before a military commission.
Bringing such notorious suspects to U.S. soil to face trial is a key step in President Barack Obama's plan to close the detention center at Guantanamo Bay, Cuba.
Obama initially planned to close the center by Jan. 22, but the administration is no longer expected to meet that deadline.
"For over 200 years our nation has relied upon a faithful adherence to the rule of law," Holder told a news conference at the Justice Department. "Once again, we will ask our legal system in two venues to answer that call."
The plan that Holder outlined Friday is a major legal and political test of Obama's overall approach to terrorism. If the case suffers legal setbacks, the administration will face second-guessing from those who never wanted it in a civilian courtroom. And if lawmakers get upset about terrorists being brought to their home regions, they may fight back against other parts of Obama's agenda.
"This is definitely a seismic shift in how we're approaching the war on al Qaeda," said Glenn Sulmasy, a law professor at the U.S. Coast Guard Academy who has written a book on national security justice. "It's certainly surprising that the five masterminds, if you will, of the attacks on the United States will be tried in traditional, open federal courts."
The New York case may force the court system to confront a host of difficult legal issues surrounding counterterrorism programs begun after the 2001 attacks, including the harsh interrogation techniques once used on some of the suspects while in CIA custody. The most severe method - waterboarding, or simulated drowning - was used on Mohammed 183 times in 2003, before the practice was banned.
WHAT DO YOU THINK? Can New York City and civilian courts handle suspected terrorists or are they so dangerous they need to remain outside the country?