Pakistan’s support to the Taliban in the 1990s had ended up bolstering al Qaeda in Afghanistan. It was not only logistics support that the Pakistani jihadi groups were providing but also manpower that was used by both the Taliban and al Qaeda. While Pakistan’s proxies, the Taliban, were well ensconced in Afghanistan, 9/11 changed the course of history. Pakistan had to face a stark choice: as President Bush put it, ‘Either you are with us or you are against us.’
That didn’t leave Gen Musharraf much of a choice. After US Secretary of State Colin Powell spoke to him in the days after 9/11 Musharraf had to bite the bullet and turn against Pakistan’s protégés. Gen. Musharraf declared full support for the United States and promised cooperation in the fight against the Taliban and al Qaeda in Afghanistan.
With the Taliban refusing to hand over Osama bin Laden, the US launched air attacks on Taliban strongholds and by the end of 2001, the Taliban government had collapsed.
The al Qaeda and Taliban leadership found refuge in Pakistan’s tribal areas (FATA) while their rank and file went back to their homes in Afghanistan. As a result, FATA became a base camp for the al Qaeda…