Just as Khalid Shaikh Mohammed was reestablishing himself in Afghanistan, Bin Laden and his colleagues were also transplanting their operations to the same country. Abu Hafs al-Masri/Mohammed Atef, Bin Laden's chief of operations, arranged a meeting between Bin Laden and KSM in Tora Bora sometime in mid-1996, in which KSM outlined a plan that would eventually become the quadruple hijackings of 2001. Bin Laden urged KSM to become a full-fledged member of Al Qaeda, but he continued to refuse such a commitment until around early 1999, after the bombings of U.S. embassies in Nairobi and Dar es Salaam convinced him that Bin Laden was truly committed to attacking the United States. Mohammed wished to retain some degree of autonomy as a mujahid. His continuing relationship with Abdul Rasul Sayyaf--an opponent of the Taliban--had to be kept hidden from Bin Laden and the rest of Al Qaeda, as full disclosure would have been problematic.
The 9/11 Commission Report notes on page 149 that KSM moved his family from Iran to Karachi in Pakistan in 1997. That same year, he attempted without success to join mujahid leader Ibn al Khattab in Chechnya, another area of special interest to KSM. He was apparently unable to travel to Chechnya, and so he instead went back to Afghanistan, where over time he became more and more imbedded in Al Qaeda until his eventual acceptance of Bin Laden's invitation to move to Kandahar and join the organization as a full-fledged member (although he claims that he still refused to swear a formal oath of loyalty to Bin Laden). Eventually, he became leader of Al Qaeda's media committee. He also worked on unfulfilled plans for attacks in Israel and Southeast Asia.