Photo shows a hijacked commercial plane crashing into the World Trade Centre in New York. AFP

In 2001 the US invaded and overthrew the Taliban after it refused to turn over Al Qaeda leaders following the September 11 attack on the United States.

Now the Al Qaeda extremist group that used Afghanistan as a staging base to attack United States 20 years ago may attempt to regenerate there following an American withdrawal that has left the Taliban in power, said Lloyd Austin, US Defence Secretary, on Thursday.

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During the course of the 20-year US war, Al Qaeda was vastly diminished, but questions have arisen about its future prospects with the Taliban back in Kabul.

This photo taken on Sept.11, 2001 shows smoke billowing from the two towers of the World Trade Centre. AFP

"That's the nature of the organization,” he told a small group of reporters in Kuwait City at the conclusion of a four-day tour of Persian Gulf states. He said the United States is prepared to prevent an Al Qaeda comeback in Afghanistan that would threaten the United States.

The Taliban had provided Al Qaeda with sanctuary while it ruled Afghanistan from 1996 to 2001.

"We put the Taliban on notice that we expect them to not allow that to happen," Austin said, referring to the possibility of Al Qaeda using Afghanistan as a staging base in the future.

Meanwhile, the new military judge presiding over the September 11 attacks trial in Guantanamo Bay said on Wednesday he would not force it toward an end — but that he wanted to see "action" after nine years of hearings.

The aftermath of a terrorist attack in lower Manhattan, New York. AFP

Air Force Colonel Matthew McCall told the military commissions court at the US navy base in Cuba, that he would not stop lawyers defending 9/11 "architect" Khalid Sheikh Mohammed and four others from making their case that the men were denied due process because they were tortured by the CIA.

Speaking just three days before the 20th anniversary of the Al Qaeda attacks, he said he wanted to move through the long-running pretrial phase of a death penalty case that has already gone through seven judges.

"This case has been going on a really long time," he told the attorneys, defendants, and family members of the 9/11 victims at the courtroom.

"I feel no pressure to get this case to trial," he said, amid defense concerns of political interference.

In a February 2020 agreement with the Trump administration, Taliban leaders pledged not to support Al Qaeda or other extremist groups that would threaten the United States. But US officials believe the Taliban maintain ties to Al Qaeda, and many nations, including Gulf Arab states, are concerned that the Taliban's return to power could open the door to a resurgence of Al Qaeda influence.