A year later Mr Mohammed joined Yousef in the Philippines for what would become known as the "Bojinka operation", a plot to blow up 12 US aircraft above the Pacific ocean over two days. That plot unravelled when the authorities found Yousef's bomb-making equipment. He was captured and taken to the US for trial and conviction but KSM escaped.
http://news.independent.co.uk/world/americas/story.jsp?story=532364

Following the attacks on the US embassies in Africa in 1998, Bin Laden gave his backing to KSM's plan. KSM was summoned to Afghanistan in 1999 and he was provided with four potential suicide operatives.

These men, two Saudis and two Yemenis, were sent on a training course at the Mes Aynak camp in Afghanistan, where they learned basic English, use of the internet and how to make travel reservations.

"According to KSM, al-Qa'idas intended to use 25 or 26 hijackers for the plot. As late as the summer of 2001, KSM wanted to send as many operatives as possible to the US in order to increase the chances for success, contemplating as many as seven hijackers per flight. We have identified at least nine candidate hijackers slated to be part of the 9/11 plot."

The report said that KSM had told investigators that as the 9/11 attacks neared, differences of opinion broke out among the al-Qa'ida leadership.

"Word started to spread that an attack against the US was imminent ... Moreover that summer Bin Laden made several remarks hinting at an upcoming attack, which spawned rumours throughout the jihadist community worldwide."

Many of the al-Qa'ida leadership urged that the attacks be called off. Bin Laden wanted to proceed. "Although he faced opposition from many of his most senior advisers, Bin Laden overruled their objections and the attacks went forward."