Sorry should have made it clearer. Mohammed Atef, Al-Qaeda's Chief of Operations, on instruction from Osama bin Laden was told to organise the the attacks that were eventually carried out on 11th September 2001. Those instructions were given in Afghanistan, those activities were carried out by Atef in Afghanistan, Al-Qaeda operated from bases inside Afghanistan where that organisation was protected and sheltered by the Taleban.

Mohammed Atta the leader of the 9/11 hijackers travelled to Afghanistan late in 1999 where he was selected to lead the mission by Osama bin Laden himself.